Well the control mechanic is somewhat necessary for most tactic/strategy games. There's nothing wrong with it once it's done well, and with a light touch. As it stands, the support style vessels are the control pieces in this game, and each one has it's own niche. Problems arise from being able to stack control for lockout of player choice (the dreaded stress+ion stunlock from 1e is a prime example, and well addressed in 2e).
Strange as it may seem, I don't really like Star Wars, but I rather love games in that universe. As such, while I know smeg all about the lore, I am right with you on the tractor beam from TIE Fighter being BS if it was directly transferred to this game. Eesh... bad times.