You can design new early game units with the traits you specify. Then the trade off comes at is it really worth that extra 30-60 production early game when you are creating 3 production, to have the traits you need for late game units. There is always a trade off and that is where the customization comes into play. Although, I find that high level early units are very good units, even with the disadvantages you bring up. Their health and weapons upgrade quite well.

There are also building upgrades and choice of experienced to get these units from level 1 to level 4 from the start.

Like parriotmath said, it is a trade off. Regular units are supposed to be different from champions that can always switch to different gear. Your experienced troops from the beginning of the game still are very valuable due to having much higher hitpoints and spell resistance compared to new troops. But they were built when your faction was still pretty "ignorant". Since you unlock and build lots of stuff that increases the base stats and flexibility in equipment of your troops you need to train new and specialized troops to keep competitive, like training special units to slay a dragon. I really don't see the problem with that.