I am one of those people who have been happy with the general direction of the game of late. Yes, there are some kinks to iron out, but I'd say there are more positives than negatives.
That being said, there are always ways that things can be improved. One such way is to make more use of the maps.
This game has sooooooo many finely detailed areas that really go to waste due to under-use and neglect. How are they under-used? Well, for starters, almost everything can be done in ESD, First City, Memory Alpha, Starbases or New Romulus.
For such a large map, that's a SERIOUS under-utilisation of the available resources. It's also VERY non-Trek. The Enterprise always traveled to do things. It didn't sit at ESD whilst Picard solved missions by running around a donut shaped facility.
I'll focus on the Fed stuff for a moment as I don't have a klink toon, but you have ESD, Memory Alpha, DS9, Starbase 39, Deep Space K-7, Drozana, Starbase 24 and the new Starbase in Tau Dewa whose name eludes me. Most of these have no purpose as everything you could want to do could be done at ESD or Memory Alpha.
Give each facility a specialised purpose, something that can only be done from there. Like DS9 before the reputation system turned it to a ghost town. Give players REASON to travel there. Want to obtain certain things? Go to this base. Want to do this task? Go to this place. Make the map relevant again!!
To add to this, make sure that unless you have maxed out your Diplomacy CXP or have a ship with specialised transwarp, make people actually travel to their destinations. The instant gratification of spending a few EC to get anywhere instantly really sucks. It makes a relatively large map turn in to a complete waste.
PWE, make your maps really count. Start to utilise the awesome assets you have. Something simple like this could really add to the game. Yes, you'll get a few people who cry that they have to spend 5 minutes traveling to their destination but by doing this you'll give us a more Trek-like experience. That's the whole reason a whole lot us play. We love Trek and want to be our own captains.
No. I consider that wandering in space is a wasted time already, even if we can doff in the meantime. I don't want more reason to do x, i just want to be able to do what i want to do without being annoyed by the 15' cooldown on transwarp abilities.
No, if anything the dependence on starbases for common tasks should be reduced further. I can't see Picard parking the Enterprise at a starbase every time Crusher runs out of hypos or Riker needs to get his beard trimmed.
More planets like New Romulus, with a bank of missions that rotate each day, so you always get something different. That would be cool (and for a double bonus, make it planets we'd actually care about: Betazed, Ferenginar). Also, make it possible to have fisticuffs on Andoria.
I agree broadly with your principle of doing more with what's there, but I just disagree on the specifics. ;-)
But forcing people to fly around the galaxy to do things that logically should be possible to do in your own ship just to make more use of the maps is not good.
No, I'd never suggest taking ship abilities away from ships just to use the map. That would be pointless. I'm referring to things that shouldn't be done on ships, like obtaining particular items, crafting, major ship fitouts, etc. Currently some locations require one or two visits for the storyline and then they're forgotten. If they found uses so that players needed to make the occasional trip (not every day trips, that would be annoying) then we could enjoy the resources of the game a little more.