I'm thinking that using all the bases on Keepsake Bay map at once might be a bit ambitious. So I've pretty much come round to your idea of making some bases uncapturable on the map to keep the game duration a bit tighter.
However, my belief is still strong in the penultimate base/"minus one" system!
So I've thought about how to combine the ideas of reduced maps/uncapturable bases with the penultimate base/"minus one" system, as well as trying to incorporate the use of Ranch and Villa.
The result is three map variations, the main one is very close to your words here:
pasik wrote:
One actual way would be by using only 3 or 4 bases from West end, Shop lane, Docks and East town.
So our viewpoints are getting closer!
Here are the map variations then. In each variation there are a total of five bases and the winner is the team that controls
any four bases. There's always more than one base to capture at a time.
Variation 1 
The main variation with best balance - the one that is similar to your quote. The winning team would therefore only need to capture the middle base trio (Shop Lane, Docks, Eastern District) or two of those three plus the opposing team's starting base, possibly by sneak attack. Or they could lose their starting base and capture all the other bases - various possibilities!
Variation 2
A little less balanced, but probably still useable. The Villa team would need to get a hold of West End pretty sharpish. Still has opportunities for the rubber boat warfare I crave.
Variation 3
The reflection of Variation 2. Rather lopsided but probably still playable.
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So there's a new plan. It combines the reduced playing area size you were looking for (and I'm now agreeing with) allied with a game mechanic that eliminates the possibility of the unwanted cases of teams fighting over a single base connection.
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Would the "minus one" system also avoid instances of "Can't respawn - last base is under attack"? Players would presumably still be able to respawn at the other base. This would be preferable, avoiding having players sit there waiting while unable to spawn.
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Another thing. There should be a colour differentiation between neutral bases that can be captured and those that can't. For example, playing on Moorland Trenches: at the start, it was all a sea of grey and impossible to see which was the gaming area of capturable bases and what was the outside zone of uncapturable bases.
I also still believe that a visual display on the map showing the base connections is needed. It would also help show more clearly the playing area. This would work alongside the targets/shields used now.
Also, I said in another thread, and Dio agreed, that the team colours on the map showing territorial control in the game generally need to be made more clear, especially the Greycollars. The grey should be deeper, like a thundercloud, so it looks as though the grey means something, as it's too close to a neutral grey at the moment and I'm never quite sure if it represents Greycollar territory or neutral area. Similarly, while less in need of a fix, the Brownpant territory could have the brown a bit more saturated/less opacity.
I suppose you're starting to run out of whitey/grey colours on the map display. You've got:
- Greycollar grey
- neutral area white (and I suppose for bases that are set as uncapturable)
- neutral area within the main playing area of capturable bases
Perhaps for the last one, of bases in the capturable area (that get captured by the teams from the start), they could be a more vanilla-y white colour so they're clear and distinct from the other neutral-y colours.