1. Well technically Pikachu tied with Latios... though it still lost to Panpour. My only guess to why they did that was to advertise the games. The only Pokemon which won in that Gym Battle were Generation V Pokemon (Tepig, Panpour, & Oshawott). The mostaggravatingthing though is that Panpour did have another reason it could have won: it knew Mud Sport. However for some reason it only used it at the end of the battle but not to reduce Pikachu's electrical attacks though more to trip Pikachu (sure it tripped out of a Volt Tackle but still when Pikachu was zapping out Thunderbolts Cress chose to tell Panpour to dodge instead of use the move which would help ease the sting if one of those quick lightning bolts hit in. 
2. I'm going to guess you say this due to Dawn being given the Everstone so it would prevent Piplup from evolving. Well another reason I don't think they used Held Items as it could be looked upon as cheating by giving it an item which increases its stats, do damage from getting hit by a physical move, making it immune to a certain type, etc.. Everstone just prevents a Pokemon from evolving, it has no effect in battle whatsoever so I guess that's why it's allowed. Also Light Ball only increases Attack and Special Attack, not Speed.
3.Apparently in Johto Pikachu was shown to know Tackle in EP118 "The Double Trouble Header" and Leer in EP150 "Hour of the Houndour". However those are the only episodes which it used those attacks (successfully) and even more interesting is that the Pikachu species can't learn those moves in the games.
4. Sadly yes, otherwise we'd spent 3/4 of the Unova Saga having Ash complaining about being lost and hungry (though Iris does seem to know her way around and can gather food). Speaking of Iris, Cilan is also being used to counter Iris's hyper activeness and insulting attitude by providing a calm, clear mind about things and serving as the mediator, mostly between Ash and Iris but if the character-of-the-day also needs it he can provide there too.
5. I suppose they wanted to have him stand out, you wouldn't really have payed that much attention to him at the beginning of the game (at least until Nimbasa City on the Ferris Wheel) if he had a normal name but a one letter name strikes youimmediately as something if off about this character so you pay attention to them.
6. Well the only major event you can "blame" them for missing is when the Gym Leaders confronted 6 of the Seven Sages. Its revealed after the game this is because by the time Bianca got to the brothers you had already beaten N and Ghetsis thus the conflict was over. Also in post story if you go back to talk to the brothers one of them will apologize for not being able to have come and help at the Pokemon League. And if you like conspiracy theories, one popular one going around is that they are actually the Shadow Triad which is why Bianca wasn't able to find them, they were already in N's Castle but they're helping the other side.
7. I don't know if the encounter rate has changed at all, you could just be unlucky. Remember, this is why Repels exist. 
8. Yeah, you'd think one of the major new battle mechanics they advertised as one of the main selling points would be used moreprominently.However this was the same problem in Ruby & Sapphire as they advertised Double Battles yet there weren't really that many. However this was fixed in Pokemon Emerald meaning that they might add in more Triple Battles and Rotation Battles in Pokemon Grey.
And what do you mean by huge? The pixels are no bigger then they are in the a normal battles.
9. Eelektross has a good Attack and Special Attack stat but is slow. I prefer Zebstrika myself as it's faster and has good enough Attack and Special Attack to do what I need it to do (though in competitive play I suppose Eelektross would be your best bet as it has good enough defense while Zebstrika will fall if you hit it with a stick).
And as for Volcarona, its good if you just plan of having it use Special Attacks though its Attack and Defense isseverelylacking and its weak to Flying (2x), Rock (4x), and Water (2x) and those types are somewhat common so it's very much a situational Pokemon.