Let me first say that I love the game. All the elements are here for a great wargame and indeed it is a great wargame, one of the best I've played.
That said, here are my ideas for improving Birth of Rome.
TITLE: First, since it is a stand-alone game, I think you should eliminate all instances of the "Alea Jacta Est" title from the game and the manual. It's a little confusing to load up "Birth of Rome" only to have "Alea Jacta Est" show up on the title screen and main play screen.
RULEBOOK: Some of the rules need greater clarity, esp Replacements and Supply. Somebody just needs to write down in plain English how these rules actually work.
Some other ideas (I hope they're not too off-base. I'm actually waiting for the next patch before I delve too deeply into the FPW as I've found it lacks balance, as another poster pointed out.):
1) Allow any army the ability to pillage an enemy region. This will have a negative effect on the NM and regional Loyalty of the side being pillaged.
2) Allow a fleet to pillage an adjacent coastal region per above. (Carth was continually raiding Roman territory prior to Rome building its fleet. It was one of the primary reasons Rome built a fleet. Historically, this is what Carth did to get Duilius to come after them with his new fleet, leading to the Battle of Mylae.)
3) Battles and capturing cities should have a greater impact on the Loyalty of surrounding regions. Low Loyalty in a region might result in a city being betrayed to an opposing army. (Many times a battle in one area caused cities in surrounding areas to switch sides. There are many examples of this from history.)
4) There should be a size requirement for being allowed to lay siege to a city. As it is now, even small cavalry units can put a city under siege.
5) Naval Combat. The two methods were Ramming and Boarding. Ramming required skillful seamanship (Carth strength), boarding required large marine contingents of tough fighters + the corvus (Roman strength). I don't get a strong ancient naval combat vibe from the game right now. You should show combat results in terms of ramming and boarding instead of shooting and boarding. (From reading in another post, I disagree that the Corvus should be tied to any particular leader, esp Duilius. He only took over the fleet because Scipio Asina was captured at Lipara and had nothing to do with the invention of the corvus. In fact, some speculate that it was, in fact, Archimedes who invented the thing. A better case could be made to tying the Corvus to an alliance with Syracuse rather than any particular leader....if what I'm reading in the other thread is true.)
6) Tie events to NM. A side could lose allies, for example when its NM falls too low. Or Loyalty values could fall or rise based on NM, possibly leading to the betrayal of cities per above. NM could be lost by having an enemy army on your soil, for another example. This would make Regulus's invasion of Africa more plausible in the game. His goal was not to conquer Africa militarily, but to shock Carth into making peace (almost succeeded) and encouraging Carth's allies to revolt. He was in Africa with only 15,000 men, remember. As it stands in the game now, even with the 2 consular armies you give him, his position is hopeless. It would be better if NM/Loyalty became a real issue for each side.
So these are my suggestions, such as they are. Thanks for a great game!