I just bought my core set and haven't tried playing yet. But from looking at the command rules, it appears that larger ships with a higher command value is considered a handicap which reflects the strict hierarchical command structure in a larger ship compared to a more flexible system in a smaller ship. Commands have to be relayed in advanced and many actions require a lead time. The watered down command tokens reflect the rushed nature of the actions in times of emergency.

Hence, are the Rebels more advantageous if they deploy many well rounded ships like CR90s and Nebulon-Bs? The Imperials on the other hand have small ships like Gladiator and Raider but they are both short range units. There is also an inverse correlation between command value and the squadron and engineering values.

Not necessarily, after you play or observe a few games you get a feel for planning what commands you need when so you can use more powerful 3 command ships quite effectively. Additionally I'm not sure why you call CR90 & Nebulon B well rounded.

You should look for posts here discussing Motti Value.

also the brb has a great engineering value

also the brb has a great engineering value

brb = Neb ?