Muv-Luv (Extra and Unlimited) and Muv-Luv: Alternative are separate games. The choices you make during Extra+Unlimited one have no impact on Alternative. During the first one, the choices you make determine the route you'll read and each heroine gets a route on both Extra and Unlimited. (Except for Sumika). To be able to start Unlimited you need to have finished both Sumika and Meiya's routes in Extra, the other routes are optional however I personally recommend playing all of them since you get more attached to the characters that way. Also the corniness of Extra stopped bothering me halfway through my second playthrough so I just went with it and ended up 100% clearing it. The routes in Extra are different from each other. This is not quite the case in Unlimited where only the ending and certain small scenes change according to the route. Unlimited's routes basically depend on one choice near the end of the game which determines which girl is going to show up in the ending. And of course, Alternative is a kinetic novel which means your choices have little impact on the story.