There's nothing wrong with the representation of hastati and peltasts in the game, AFAIK. It's true that a counter to peltasts was developed - perhaps these are the "heavy peltasts" in RTW. I believe in RTR 6.0, they will be called Hypaspists. You are right about Rome's starting position not including Sicily.

If you are interested in historical accuracy, I'd recommend the Rome Total Realism mod. It fixes starting territories and units to be more historical. Also have a look at the Europa Barborum forum here and read some of the weekly faction reviews - they have very informative descriptions of units.