I think this topic has been knocked around a bit before.
But now, with Second Edition well circulated, players are experimenting with new ships and it makes sense that it would come around again for further discussion.
Personally, I'm a huge fan of counters all the way. They are a part of the reason I got into this game. (With my limited experience in 'table top' gaming, I have yet to hear of another game out there where counters and tokens are 100% acceptable in any "official" game play.)
Granted, not all the new ships and fleets have counters yet.... (I specifically say "YET" as to encourage Mongoose to continue providing counter sheets... <hint!, hint!> ).... but with a few well placed substitutions, one is capable of carrying everything needed to play any fleet in one, single, easy-to-carry box! (Again, in my limited experience, the expense of mini's seems to limit players to one or two fleet for constant play. While I tend to favor the VREE or even the RAIDERS, I don't necessarily want to play them, especially the Raiders, all the time.)
My aversion to miniatures is mostly an issue of space. Or more precisely, lack there-of. (No place to work on them. No place to store them at home. Little room in the car to transport them.)
The mixture of "capital ship" miniatures and "counter" fighters does seem to be a good compromise though. With fighters moving last, it's sometimes helpful to have the flat surface on the gaming table so movement of miniatures seems less cumbersome. (...no easy way to describe that, but anyone that's played that way knows what I'm talking about.)
There is my totally unsolicited opinion..... It may seem like petty reasoning, but I tend to find the most practical issues usually wind up being the greatest influence on us.
-Mister_ELK