Six years of WoW has made me gun shy about visiting game forums so forgive me if this has been proposed before.
I try to keep up with the dev chats, the Q&A's and the handy engineering reports, so I understand the improbability of being able to implement a system of combat and on ship travel through sector space. The engine just wasn't designed with that in mind. However, I really think this game needs some type of on ship travel system. Yes, I know this is a game and it's not meant to be an episode of Star Trek, but let's face it, the vast majority of Star Trek takes place on the ship. Without that component in the game everything feels unfortunately less Trek.
So. What I'm proposing is an on ship sector space travel system that is removed from the actual sector space. For instance: You're in the Sirius Sector Block and need to travel to Risa. As of now, most of us will open our map and auto fly to Risa. This often requires manual course corrections to avoid enemy patrols. My alternative, which would be completely optional, would consist of you going to your bridge and speaking with a BO or interacting with a panel. This would pop up a list of the systems from the sector you just left. In our case you click on Risa. The systems screen disappears and you get a message from a BO saying the time it will take to travel. The time could either be the actual time it would take, ie 2-3 minutes, or it could be the relative time it would take if you were really traveling in space. I suggest that mainly for people that don't want to be taken out of the immersion. Since a trip to Risa from the Sol system wouldn't actually take 2-3 minutes. There could even be a time frame added to the current UI displaying the time to arrival. Keep in mind this travel is completely artificial since the current game engine isn't designed to allow on ship sector space travel. In actuality you'd just be sitting on your ship for a period of minutes before the BO pops up and says "We've arrived" then you can click the option to load into the system you travelled to. However, this isn't much different from the current, "click on Risa, go make something to drink, come back and continue." I'm simply proposing this as an alternative that would feel considerably more Trek. Not to mention that once more options are added to the interior of your ship this system would allow you to play around with them before arriving at your destination.
This system doesn't have to do away with deep space encounters either. There could always be a random chance to be attacked. In which case you'd simply load into a current DSE like normal instead of loading into the system you were headed to. I would prefer a low chance, something like 10% or less considering that the vast majority of people avoid enemy patrols to begin with... they're just not fun to get sucked into unless you're looking for them. I'd be fine with no chance of random encounters, but I know others wouldn't and that's perfectly fine. Like Cryptic loves to say "this is a game."
Anyway. I don't know if anyone else would be interested in a system like this. I'm just a long time Star Trek fan and really hate that portions of this game feel so un-trek. Granted it has improved drastically since the game was released last year.
I think that the devs likely want to avoid removing players from the Sector maps, as this is the only place they can interact with each other, and the environment. Enemy Encounters don't work very well, they are too easy to avoid and too time consuming if you don't, but I think the devs want to implement something different, either random encounters with ships or with Nebulas that you could choose to explore. So I think the devs would rather not give the players the option to skip that altogether.
On the other hand, when travelling from far on the other side of the map to Earth Spacedock, unless I choose to use my Transwarp, it does get tedious to travel the other side of the map, zone, travel to another map, zone again, and so on. For those kind of long trips, I think it would be helpful, and not too outside the current style of play that it make normal Sector travel unacceptable.
In other words, if you are travelling somewhere in the same sector, no. Going from Earth to Risa you would not be able to go to your Bridge. On the other hand, if in Sirius Sector you might go to your bridge, and find a number of options displayed on your helm like "Deep Space Nine", "Memory Alpha", "Romulus", and so on. Maybe one or two locations per Sector Block, but otherwise similar to the Transwarp system for Diplomats. You make the selection, and you proceed to that system. On arrival, you are told you have arrived, and can leave the ship.
In short, you "jump" from the old Sector you left when you entered the bridge to the new Sector after a given amount of time. You in essence have a loading screen to get on your bridge, and then another when you reach your destination. You might be "locked" in the ship while at warp, (so the game doesn't have to compute how much progress you have made) or if you abort the trip you could just end up back where you started.
The option of random encounters and nebulas could still come up. But since it is "long range" travel you don't have two ways of doing something, one of which might be more convenient or safer than the other. BTW, Transwarp would still be useful since it is instant, and this would take time.
If you really want to make it interesting, you could be required to fly to the border before "going to the bridge" and when you reach the destination Sector you would enter at a sector edge, and have to return to the Sector Map to reach your ultimate goal. This would be pretty ineffective if you were just travelling to an adjacent sector, though, so maybe it would be limited to jumps of two or more sectors.
That is, when you reach the edge of a sector, there could be a choice between "Go to Sector X" and "Go to Another Destination (via Bridge)"
I can understand the concern with wanting to keep players interacting with one another. However, sector space is by far the only, or best for that matter, way to interact with others. There are ground maps, stf, fleets, and the team finder for that kind of thing. Plus, I'm not suggesting that my current system replace the old sector system. It would be completely optional and dependent upon the types of players using it. I mean if you're flying from Sol to Vulcan, I can't see loading to your bridge, then waiting for the trip to be very efficient. More lore and role play friendly, sure, but again I can't see most people doing that for brief trips.
I do like your idea of long trips, though. In my opinion neither will really take people out of sector maps a great deal. You'll have the role players that use the function a great deal, the casuals that use it when it's more convenient, and the people that simply like the current design better.
Either way more effort needs to be put into making interiors useful. I'm afraid that Cryptic is going to rely solely on Foundry creators to make the interiors useful. While the Foundry is an incredible tool, it can't replace developer created content.