1) Why did Itachi not kill Orochimaru?
For someone like Itachi his younger brother meant the world to him. More than his clan and more than the village he spent his whole life trying to protect. Itachi should've known that Orochimaru would one day go after his younger brother Sasuke to try and steal his body. I guess Itachi knew that Orochimaru would never kill Sasuke as he sees him as too valuable of an asset to kill. Also by the time Orochimaru would finally be able to steal Sasuke's body that Sasuke would have developed his sharingan enough to defeat Orochimaru.
2) Why did Orochimaru not try to steal Itachi's body when he was a kid?
In Naruto Shippuden there was a flashback where Orochimaru saw Itachi training and saw the power of the sharingan first hand. He saw that he could use the sharingan to develop his mastery of jutsu more quickly and possibly perform other jutsu outside of normal means. He could do all this beyond only seeking the power to prolong his life. However, I imagine the reason he did not steal Itachi's body when he was a kid is because he had not learned how to perform such a jutsu yet. Otherwise he would have attacked him then and there.
3) Why did Orochimaru not just get the sharingan implanted into his eyes like Danzo and Kakashi?
I imagine early on or at least at some point he saw the limitations of the sharingan to someone who was not an Uchiha. For example, Kakashi has to keep his left eye covered or else the sharingan will continuously use up his chakra. Someone not born with the sharingan can not turn it off. Therefore, if it was implanted in both eyes the user would have to walk around blind until a time came when they would need it's power otherwise the power would use up all of their chakra. As a result, it could cause them to die when their chakra is at or near zero. Also the sharingan uses up more chakra and can leave the user extremely fatigued if the shinobi is not an Uchiha. For these main reasons Orochimaru saw that it would be better to transfer himself into other people's bodies to fully utilize their powers and not be crippled by the limitations of having those abilities transfer to someone not born with them.
4) Why did Naruto come back to the village with practically the same ability and skill as when he left?
For someone looking to become the strongest ninja and most regarded shinobi in his village he didn't change much in two years. Sure, he has a new outfit. Sure, he has gotten taller, and has a deeper voice. However, beyond that he hasn't changed much it's almost jarring. I guess because Jiraiya only taught him some of the fundamentals he needed to work on, such as, better utilization of his shadow clones, genjutsu, improving the rasengan, and harnessing the power of the fox. He could have taught him so much more though, such as sage mode, controlling his anger, developing his intellect, finding his chakra nature, training to improve his taijutsu so he doesn't have to rely so much on his clones, training to use the rasengan without his clone, and so on. All these things Naruto really should've worked on or at least been told by Jiraiya to work on. I would imagine the reason why they didn't work on these things is because Jiraiya travels around a lot and he writes his book, and is off doing whatever sometimes. As a result, Naruto could not get as strong as he could've gotten and Naruto isn't the type of shinobi to figure these things out on his own. He often needs someone to inform him of his weaknesses so he can even begin working on them.
5) Is it me or did Naruto seem smarter in Part 1 then in Shippuden? At least comparing the beginning of both series.
If you go back and watch like the first 2-3 arcs of both series you will see that Naruto as a kid seemed smarter than Naruto as a teenager. Kid Naruto was more clever while the older Naruto seemed a bit more impatient and quicker to fall into obvious traps. Like that time Deidara baited Naruto into following after him even though it was an obvious trap. I mean don't get me wrong Naruto has always been slow to pick up on things, but you'd expect with age comes experience and a little more common sense. In part 1 when he was taught the rasengan and summoning jutsu he had to be told once what to do and he understood. In part 2 when Kakashi and a few other characters were instructing him he often had to be told multiple times how to do something or what was going on. This was to the point where even the viewer along with characters would get annoyed with Naruto. I guess this is because Naruto is a visual learner. In order to learn something best he has to be told and see what it is in the same breath. Also the reason for more of his overactive impulses in Shippuden I believe was because of the influence the nine tailed fox's chakra had on him after prolonged use over time.
6) What was the Illness that killed Kimimaro?
Kimimaro said that he raises the calcium in his body to make his bones harder than iron and to make any number of bones. Excess calcium intake may cause muscle spasms, the calcium may appear as unwanted deposits in organs and tissues, such as bone spurs or plaque in the wall of blood vessels or in kidneys, heart, and liver, and it may increase the risk of cancer and cause other symptoms, including migraine headaches, pain, kidney stones, depression, and heart arrhythmia. It could be that his kekkei genkai has similar drawback like that of the mongekyo sharingan. The mongekyo sharingan causes the user to eventually go blind after prolonged used over time. However, if the user implants normal sharingan into their eyes then the power of the mongekyo can be used without drawbacks. I imagine because he was always trapped in a cage and never knew his clan or the history of his clan that he never got to know how to properly use his power or circumvent the possible drawbacks of his ability.
7) Where was Danzo in part 1 of the series?
In part 2 of Naruto, Danzo just sort of shows up as a random antagonist. There is no mention of him, suggestion or hint of him in the original series explicitly. The reason Itachi shows up in the village in part 1 was to warn Danzo that he is still alive and that if he did something to Sasuke then the entire village would pay for it. Danzo is always doing things in the shadow so there was no reason for him to be there. Also to explain why he didn't take over as Hokage when Hiruzen died is because the elders saw the Sanin as more fit to rule as Hokage and Danzo's characters was still being written by the creator Kishimoto.
8) Why did Kakashi not use the mongekyo sharingan in part 1?
In part 2, looking back at a flashback in Kakashi's past we see he awakened the mongekyo sharingan after killing Rin. Since he activated it as a kid it would make sense for him to use it as an adult. Maybe he didn't use it in part 1 because he was still dealing with the regret of how he awakened the power which was by killing his fellow teammate and friend Rin. Maybe he could not deal with the strain of using the power of the mongekyo sharingan. I mean using the normal sharingan in part 1 after a drawn out fight left him bedridden for a few days. The mongekyo sharingan would take an even bigger toll on his eyes and his body so who knows how bad it would've affected him. The most probable cause is Kishimoto had not written this into Kakashi's past yet.
9) Is there a slug based sage mode?
In Naruto Shippuden we see both a sage mode for the snake and a sage mode for the frog, but there is no mention of a slug based sage mode. Tsunade does not have sage mode, but she has her 100 healing jutsu in which she uses chakra she has stored in the back of her forehead to increase the rate at which cells can be reproduced. As a result, this allows her to recover quickly from being wounded for a period of time. I don't think there is a slug based sage mode or if anything it wasn't written into her character because sage mode represents power while Tsunade is a healer. If the creator gave her a power up like sage mode it might take away from where she shines the most which is as a medic. So in order to enhance her fighting skills while retaining what she does best she developed the 100 healings jutsu.
10) Why did Minato not use sage mode while he was alive?
Minato the 4th hokage has always been called a genius so for him mastering sage mode should be a piece of cake. Well, I believe for him as a character and as a fighter sage mode wasn't a good fit. Sage mode takes time to master and to build up chakra. It's also easier to learn if you have a lot of chakra like Naruto. Personally, I don't believe there was ever a real reason for Minato to utilize sage mode as his fighting style revolved around fast flashy precise attacks. Sage mode revolves more around stillness and raw power which isn't really reflected into his fighting style. The only reason I can see for him taking the time to even learn it is for combat versatility and if a threat ever came that he couldn't handle under normal circumstances. (i.e. Madara in the war arc) If that ever happened then he could utilize the power of sage mode to take care of it. Also the reason the reason why I believe he could transform into sage mode so fast during the war arc is because of his reanimated body which gave him unlimited chakra. Allowing him to take in nature energy more quickly.