RTW, going from memory:
1. One of the bigger aspects that was missing in RTW was the total absence of troops armed with thrusting spears AND throwing spears. Instead RTW had fantasy units like head hurlers and wardogs. Too bad, because it would have been nice to fill out the balance with some melee troops carrying thrusting/throwing spear combos.

2. The whole animation for hoplites is questionable, I've been convinced by others here (and reading, and looking at contemporary depictions) that hoplites indeed fought mainly overhand. Underhand was used, but not as the primary style.

3. And the Macedonian style phalanx animation suffers from not being shown two handed and not being positioned properly. The shield position is an issue as well.

4. Another one that is annoying is that the wrong elephants are used. Large savannah/bush elephants are incorrectly depicted for the two better elephant types. However, both of those should use Indian elephants. The smaller North African forest elephant is depicted for the base elephant unit (correctly.) The forest elephant is the smallest of the three types, with the Indian elephants being in between, and the big bush elephants being the largest but not being trained for warfare.

5. Another thing missing from elephants: the Numidians didn't use towers on them (nor did the Carthaginians most likely, since they also used forest elephants), but did have a rider or two sitting behind the mahout and hurling javelins.

6. Ditto for the British chariots. They should have been javelin hurlers who dismounted to fight--essentially elite mounted infantry champions. Granted, this latter part is hard to program. However, the British archer chariot units are just wrong.

7. Flaming arrows--uggh. Too mobile, used too much by the AI whenever it sees a unit with weak morale. They should be much more problematic, and restricted in employment. Certainly should be unavailable in certain types of weather. Easy to edit out...

8. Archery--big problems. Range is too high and killing power much too great for base level units. And elite units have far too much range. No clear attenuation of accuracy with distance. No lack of line of sight issues that would kill accuracy. They can all fire even when 16+ ranks deep. Weather effects very muted.

9. Vanilla slingers should have a bit more range (while vanilla archers should have less...so both would be similar in range.) Best to adjust velocities in the files too if you change these.

10. Light auxilia are depicted with pila instead of javelins...merely a cosmetic issue.

11. Would have been nice if the Romans had a slightly weaker assortment of hastati/principes at the start. Historically, they adapted during the 2nd Punic war to the gladius. Before that their swords were less effective. The Iberians (Spanish) had better iron and smiths, so the Romans adapted from them. Also, during the time frame of the 1st Punic war and into the second, they perhaps should have a somewhat flatter more oval scutum instead of the larger curved later shields depicted. Also, the Romans were only using a single greave at the time (lead leg.) In all this isn't a huge difference, but the early hastati/principes should have their hands full against Iberian troops who had better swords.

12. The stats of the Iberians don't match their gear...despite having decent protection shown, they've been given almost no armour (less than many barechested/bareheaded units.) And compared to the hastati/principes their swords are not given adequate stats. It is unfortunate, since this is the only sword unit the Carthaginians have, and it is really useless. It is difficult to get to the build level of even Libyan spearmen for many cities early on, so this really weakens the Carthaginian stacks--can't be helping in autocalc for AI vs. AI.

13. Rome should get access to slingers (funditores) , rather than an archer unit prior to the reforms, or at least earlier in the tech tree than the archers (which would be moved back a notch.) Note also my comments about the relative merits of archers/slings in this period.

14. While it isn't a "mistake" per se...an eariler Italian campaign with Samnites, Latin League, Etruscans, Epirotes, etc. could have been very interesting. It would have required greater speculation on unit types, and would have been smaller in scale. But this would have allowed the Romans to field a rather different initial army than the Polybian legion...perhaps even hoplite style, then have a trigger event to adapt.

I can forgive the Egyptian depiction to some extent, the units might not look right time wise, but there are several phalanx units. They also have access to elephants if memory serves. Several of the depictions are pretty decent, except for being out of the timeline. The Egyptian chariots...well, those of course are more of a problem. So anyway, I'll grant some leeway for the Egyptian units, as they at least have some basis (although anachronistic.)