My guess is most people see Rome Total War (vanilla/first) as a far better game. I would simply want to see more enhancements from the first engine - just by paying attention to detail - you wonder if certain features could actually be useful...
In RTW;
Any General/Commander leading an army has the option to bring up to 20 agents - this is almost never used by anyone (atleast - they might bring 1 of each possibly). Historically - Generals/Commanders would have a set number of spies, they many have personal bodyguards, assassins (or some kind of small elite force for infiltrating at night - assassins do destroy settlement buildings in RTW) and they may likely have more than 1 diplomat (at-least if they're important)... Generals have stats - Command, Management, Influence... What if - the more assassins you had with you - the better command your general has (because say anyone who didn't listen while marching - was taken around the corner and dealt with), the more spies you have with you - the better the management (they could have some intel on what the men want and need), the more diplomats you had with you - the better influence (they could be somewhat advisers before a speech)... A new agent suggestion would actually be "commanders" which could be made essential to leading an army - they could be one day promoted to a general (you decide based on their highest stats and their necessity) - they could also have a role in dealing with corruption in cities as they'd have some power in leading troops around the city unlike assassins who work solo. (since corruption is something you're very limited in controlling). So after all this you might have something like 5 assassins, 5 spies, 5 diplomats & 5 commanders in your leading forces on the campaign map.
In RTW;
You have bonuses for spearmen but no one else in mind (spear, light_spear, spear_bonus_x)... I have tried with great difficulty to come up with a system where axeman are specialists for dealing with spearmen (through having more mass and being more defensive than offensive than say swordsmen) - the motive for this change is - axes cut wood better than swords, and spears can't cut spears... if axemen were passively attacking a phalanx they'd damage the spears - I'm not suggesting they were historically effective in this way - but I'd imagine that the phalanx's would have more concern over these troops. I tried to make swordsmen a clear counter to axemen while being some kind of intermediate troop - I attempted this by giving them more attack speed (so they'd clearly be favourable against axemen but wouldn't have the mass to push a phalanx - I didn't want them to be completely whipped off the floor by phalanxes immediately as I tried to make it so they can pull back without being completely softened)... I tried to make spearmen (none-phalanx) as the "fill the gaps" troops... I powered RTW through the BI engine and gave basic spearmen the shield wall formation to for-fill this roll. I also made a spear-men specifically designed just for cavalry (with the schiltrom formation) and as a result were weak against about nearly every other unit but less-so swordsmen... and phalanx's I just tried to nerf to do less damage so quickly - so that you can pull troops out asap. The whole problem with all these changes is that - once I tried making the next tier of troops... each previous tier reacted to different to what they're supposed to do. Sometimes the lower tier swordsmen were better than the lower tier axemen at dealing with higher tier phalanxes as an example due to how the swordsmen had a higher damage output by hitting faster. It became too difficult to balance what I want to achieve and the RTW engines can't accomplish this. So other bonuses more simply I'd like to see are... "axe", "sword", etc... "axe" could have the bonus of boosting lethality against spearmen by 10% or so... "sword" could have the bonus of boosting lethality against axemen by 10% or so... there could also be "axe_bonus_x" and "sword_bonus_x" where you could choose your lethality specifically. Added bonus options such as these would have resolved the issues I was facing.
More In RTW that I would have wanted to see;
You could combine two none-full unit troops... but you couldn't split them, the AI in Barbarian Invasion didn't use the shield wall... Cantabrian Circle only worked for missile cavalry troops (you might be thinking - hang on, that's how it's supposed to be - but the intention i had was to put it on chariot troops - the idea was to get the chariots to surround an enemy infantry unit so that they were stuck behind spiked wheels running around them which was likely an employed tactic itself, I mean... I see it far more effective than putting your horses at risk of being attacked by charging them into the unit... It probably deserves it's own formation but like-wise I would have liked the engine to support this. Another limitation was that missile chariots could only use archery if you wanted the men to move in animation as they fire - javalin firing chariots were a thing in briton... something else I wanted to create was head hurdling men on chariots who could potentially run amok (1 of the heads could fall on one of the horses if the chariots were being engaged enough for a situation to create that). Other limitations included - not being able to destroy watch-towers (including your own if you wanted something neat looking)... I also think the barbarians deserved their own their own kind of deployable building that was like a semi-village of sorts where you could train basic troops from (and retrain better troops from) - if the local settlement was large enough to support this - this is so barbarians are less "boring" having less abilities than their neighbours. Why not make the locals in the lands feel more aggressive - this could also be a solution for other things such as population control etc -perhaps these small towns you create aren't taxed but an amount of population can live there - if your main settlement gets taken over by rebels - you can train at these small towns to take it back fast.
I'll probably end these thoughts here - there are just problems with RTW when paying attention to detail that should have been evolved from imo... RTWII was the wrong direction of trying to rework everything... RTW should have Imo been evolved from... it was far more user friendly - saying that, I'm not against a lot of new ideas RTW may have brought that didn't limit what you could do compared to RTW.