Let's look a little more closely at this notion of environmental phenomena and how they can affect tactics.
1. If some environmental phenomenon degrades sensor effectiveness, then it ought to honk up the sensors of everybody who's there. (Unless you choose to make some kind of sensor effectiveness tradeoff -- maybe your ship has more power to pump into your sensors, but the increased power usage lights up your ship like a terawatt Christmas tree.)
The point of having environmental capability degraders (like sensor-masking nebulae) isn't to allow smaller ships to terrorize bigger ships at will. It's an equalizer. By temporarily disabling certain capabilities of everybody, ships that are smaller or damaged or are commanded by less experienced characters stand a fighting chance against a bigger, badder enemy.
2. I see lock-ons versus "run-and-gun" as the difference between thoughtful RPG combat and action-oriented FPS combat.
Speaking for myself, I would much, much rather see the style of space combat in a Star Trek MMORPG be determined by the mass of one's ship. If you like to "shoot from the hip," then take a smaller ship and zip around all you like, firing manually at anything as soon as you feel like it. You won't have the protection of a bigger ship, but the action will be a lot more intense.
If your interests run more toward defense, or toward being able to intelligently use multiple systems to achieve victory, then you ought to be able to choose a bigger, slower ship. While I'd expect these ships to be more heavily gunned than a smaller, nimbler vessel, the price is that you'll have to take the time to maneuver to achieve an optimum firing solution. You'll turn like a scow, but you can hang much longer in a firefight and do more damage to acquired targets than smaller ships.
I'd really hate to see Star Trek Online pass on a balanced game like this in favor of one that's all twitch-mode, where the environment is so sparse that there are only two tactics (fight or flight) and the choice between them is trivial. If the space part of a Star Trek MMORPG is as important to potential subscribers as the Perpetual-commissioned Nielsen survey from 2005 suggested it was, then I believe space combat needs more tactical depth than run-and-gun alone can offer.