Graphics "can" be one of the biggest things to change as the engine can work in a state that enables them to work on gameplay with things missing, high res textures not made yet, a basic lighting engine to be replaced with proper lighting and lots of effects and so on and so on, with more detail being enabled as things get added and as the engine is optimised so theres more power available.
A very early beta I wouldn't judge on graphics, nor too much else to be honest. Though is possible for a beta to be so crap they stop it, start a major new overhaul and completely change a game considering the amount of trouble its had I'm not sure you can expect that this time around.
I honestly can't see them making it even close to a perfect game though, its just too much to do when you try too many different things. Look at how many MMO's fail when they only have one area to focus on, Warhammer, ground combat, fairly small world, lots of easy limits to place on time and where the effort goes. A game where you're trying to make two entirely separate games basically in one will never have the time needed to make both perfect, if you want one part to be great I'd expect one part to be pretty dang basic. The sheer amount of worlds you should be able to visit to have missions and storys also makes it difficult. Imagine every zone in WOW, slightly different, but do you choose to only let the ship visit 20 different worlds? use the same map for multiple different worlds, have similar enemies wildlife almost everywhere, or 100 worlds with slight variations, how big do they make the area on each world.
Frankly I can't see the game working unless a Roddenberry of some sort decides to cash in, throw in millions for developement and make a fantastic game that won't be out for years which is a huge shame.