Ok, lets clear one thing up.
There is no 'proper historical formation' per se. I agree that when it was convenient the 3 line formation was respected. But most generals that were at least 'ok' decided on frontage based on what they were seeing on the battlefield. There was great concern on ancient battlefields of getting the 'flank turned'. So frontage was always of primary consideration. And there are frequent historical references to deploying troops so as to prevent just such an occurrence. Even with Roman articulated-manipular infantry, fighting in more than one direction was just bad.
It also seems that different generals had different opinions about where their more questionably mercenary auxiliaries should go, so that isn't even clear cut.
What was 'preferred' is not always what was 'used'. Its all about practical application.
So adjust your frontage so that the Gauls can't turn your flank, and use a reserve of one or two cohorts to plug the gaps. You can revert to 3 lines when your frontage allows that (just like most Roman generals did) and still respect history.
Given the very slight difference in Hastati and Principes in the game, I tend to run w/ 8 Hastati and 4 Spear Mercs then Triarii afterwards. I play just as you do, but adjust frontage accordingly (just like ancient generals), and find my guys do fine. The game's mechanics even supports identifying the 'veterans' (since they show up as 'chevroned' hastati infantry). So when deploying in 3 line formation, I put my more experienced guys to the rear as my battle reserve. This works really well because they provide just the right amount of shock at typically the pivotal moment in a battle (when all lines are fully engaged).
The truly great generals of ancient times showed one quality above others which made them successful. They adapted to what they saw.
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