Simply put: The episodes are for replay value with multiplayer being the end-goal.
Due to the fact that the AI doesn't become any more intelligent (they're already dull enough for most seasoned strategy gamers), they need to handicap whatever Pokemon link you have access to. This isn't a hindrance, as it would only make the game far easier if you had your 88%-link Raichu on the field - it's a proper handicap to make the game continuously challenging.
And you actually *DO* get to use them: The Gallery is used for multiplayer.
Whatever you had recorded into your Gallery, is accessible when you go against someone in multiplayer. It's a Pokemon game in the end: focusing everything into multiplayer. That "pokedex" is useful.
And honestly? It only encourages you to take your time with the game and build up your teams. I may have to start with a 10%-link Raichu, but it's still a Raichu - easily a threat for any Water Types even on the 40% range. It's paying me off for my hard work to evolve the pokemon during my playthroughs without making me overpowered.
In one argument: It's a strategy game. Take your time. Make your decisions. And realize it will have some consequence in the end. Those lower-ended generals will be your main forces in the next playthrough, so don't ignore them. And those higher-ended generals will be your prizes in your attempts to obtain them during battle.
In the other argument: It's a pokemon game. Realize that in the end you're building your forces to beat another player's forces - not really to max out as a strategy game. And if the link percentages are reset, it doesn't matter: You can set a link handicap in the vs., effectively equalizing whatever advantages and disadvantages one had in creating their teams.
EDIT: Also, after playing through a session of mutliplayer today... I found out that you *DO NOT* lose any of your Link % in the Gallery. It may change when playing through the bonus stories, but it *DOES NOT* change for the Gallery. In fact, I think it *ADDS* to your Link %. As in: any Link %s you gain through the side stories may be added to your highest Link % already placed on your Warrior.
Also, and this is just an assumption, but there may be a chance that you CAN play through the main story again. In a New Game+ fashion, that is. ... just an assumption, nothing yet founded since I haven't quite looked for it (busy as I am with my post-game fourth side story). But simply saying that so you don't count it out completely... like how you counted out Link %s ever being kept. Perhaps after completing all the Side-Stories or simply hitting the "New Game" button will accomplish this? Don't quite know yet. Will edit and update when/if I figure it out.
***EDIT EDIT***: Yep, if you want to play the main story again as your main character: You must complete all the extra story missions.
Troublesome, but kind of makes all your negative points moot.
Still, the extra story missions aren't too troublesome. With all the benefits you gain from each mission (extra pokemon, extra generals, extra chances to improve teams, and legendaries), it's well worth it.