Honestly, I'm sorry, but I disagree with you at almost every turn.
A. Sidekicks have to go through everything you do:
Okay, this one I will give you...most of the time. But there are quite a few characters who don't have to go through what you do, one of them being Navi. She has two big advantages you don't, one being she can fly, and the other being she's very tiny. All of those traps you have to slog through, If we were playing Navi, 90% of them we could get by just by going forward. Sliding spike covered things zinging across the floor? No problem. Have to hit a switch on the other side of a wall by sending a Bomb-chu through? Just fly through the area the Bomb-chu would fit through and bam, you're done. Admittedly she can't fight all the enemies, but that just gives more props to Link, since he has to solve all those puzzle and kill the enemies, and that brings me to my second point.
B. She's necessary for battle:
Okay, honestly, this isn't true for two reasons. First being the fact that the next to last battle, against Ganondorf, you go through without Navi and I did just fine, thank you very much, as I did against Ganon (considering she kept targeting his face, it was just easier swinging at the tail myself). Secondly, that must mean that all the Links that came before and after the OoT one must be exceptionally better swordsman than the OoT (and MM) Link, since all of them seem to get through their adventures without needing any glowing light to target their enemies.
C. Navi is your conscience:
Okay, this one I just don't get. How is she your conscience, external or otherwise? Because she tells you to where to go in the next step of the game? The step that was blatantly obvious and that I was going to do regardless? Yeah, that's not being a conscience, that's just being redundant. There are no moral quandaries in OoT, as far as I can remember, so I honestly have no idea how you justify calling her an external conscience.
There are other arguments I could bring up, and I'm sure many have before I post this, but these were really my biggest concerns. All in all, most of your arguments were based on flavor rather than substance and, truly, Midna was far more helpful in TP than Navi was in OoT, and even Tatl, though having quite bad attitude in the beginning, was far less annoying during gameplay.