I don’t think there’s anything necessarily wrong with generic as long as it’s well done and not a complete clone of an existing game. That faction upgrade system sounds like it’s enough to offer a unique experience and make your game stand out from others in the genre, and there’s plenty more you can do with small mechanical decisions to make your game feel different from existing games. Whatever the theme or gimmicks, I think the best strategy is to focus on the fundamentals and just make a really solid RTS game.
One problem I see with the second one is that it sounds too much like rock/paper/scissors, not in the sense of having a combat triangle of counters, but that by separating the production and battle phases, players will have to blindly choose a tech path and hope that they picked the right one to counter the other player, since they’d have much more limited opportunities to switch builds after seeing what the enemy is doing. It sounds like it’d run the risk of being too much of a simplification of the genre, and that could turn off the core RTS gamers who would otherwise be the main audience.