I am a bit torn on this issue and have varying opinions on the matter.
I can understand the draw to and the enthusiasm for nextgen graphics, and as was stated previously, ST:O would seem a logical game for nextgen graphics. Anything that gives the player that extra bit of immersion, to make them feel a part of the Trek universe can be a good thing. However, this also presents complications in the form of hardware and the ability to attract a wider audience and draw in as many people as possible. Hardware upgrades to a PC to support nextgen graphics can get expensive, and for some people, could mean the need for an entirely new computer system. This will often limit the people who would be drawn to a game to just the hardcore fan base as most gamers will not justify upgrading a system for one game. Furthermore, this puts the devs in an akward position because they want as many people to play their game as possible and requiring massive hardware upgrades won't make that happen. On the backend of it, next gen graphics can also present server based problems as it slows upload/download times and can be overwhelming for an online game. This will increase the lag factor and possibly create bad mojo among the players of the game.
On the other side of the coin, stylized graphics can have major benefits, but with those benefits come drawbacks as well. Stylized graphics allow the devs to produce the game faster and produce a higher volume of graphics, which can mean more content and a faster release date. If using stylized graphics is the difference between us seeing only the Alpha Quadrant (with nextgen graphics) or all 4 quadrants (with stylized) at the time of release, I might be inclined to lean towards the stylized as it allows for more immediate exploration and fewer massive patches and expansions. However, the drawback is that with stylized, the immersion factor is reduced. If we are playing a game that feels too comic book or to WoWesque, then the immersion into the game will not be the same, and instead we end up playing the TAS version instead of the TOS version. (only as reference and comparison of animated vs live action)
In my mind if the devs go with a stylized look, it will need to be a nextgen stylized that is a step beyond the WoW look to remove the cartoony factor. Otherwise, they are better off going with a nextgen graphics styling and hope that it will not drive away customers and severely increase the lag.