I've always prefered counters. Personally I don't really think of the game as a mini's game but as a wargame. I find it a funny quirk of marketing/history that the game has such a strong mini following when I would have thought it would do great in the wargame community. I understand that mini people love their minis and this game has great ones (despite some of the quality issues) but the counter availablility always made it more accessible as a wargame. Battletech (especially original non collectable) while being a famous minis game was always at its heart a wargame that you could use minis for instead of counters (hell they even used hex maps).
While the mechanics of ACTA don't scream wargame, I find (as a predominantly wargame not mini guy) the counters give a completeness that wargamers would find appealing. As you know one of the main appeals of minis is collecting your favourites and painting them, giving them the love they deserve. We wargamers on the other hand tend to be a lazy impatient lot, we want to be able to open it, read the rules and play. None of this preperation nonsense. Also wargamers tend to like the idea of "the complete game", having all the parts needed, both players are equal, one doesn't have an advantage because he can buy any minis he wants, and you can't get that one piece that would make your perfect fleet complete because you can't afford it till next month. The presence of counters, especially in the 1st ed box set gave that sense of "I have everything I need, I don't need to buy stuff for the next 6 months". I was surprised to find counters not getting a look in for the last year or two, no dilgar, or drakh, or armageddon stuff, no 2e stuff (but coming soon
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ACTA may still do well marketed as a wargame rather than a mini game. While I feel very sorry for you mini guys out there losing some great minis, especially the ones who wouldn't really consider playing with just counters. I think ACTA could do well as a wargame, there have certainly been successful wargame battle games before (Battletech, Star Fleet Battles etc). The only potential problem is ACTA is now firmly thought of as a mini game, but perhaps a bit of new marketing, perhaps a box set of rules, fleet lists, counters like 1st ed could get more wargamers into the arena.