Alright, so i have completed both and these are the only real differences i have noticed.

Whiterun - stormcloaks attack / imperials defend
your rank - imperial gets actual rank ( legate ) stormcloaks get nicknames (stormblade) these are the finals
what you get from leaders - stormcloaks (general armor) imperials (deadric sword of leeching) these are the finals (for killing final enemy i am not completely sure the weapon is always the same, i was a level 50 when i got it and i had daedric unlocked.
their are no real differences between them. i still have not received or found the badass imperial armor, the one that looks like Leonidas helmet or Achilles helmet, i am currently looking for it.
thats all i have really noticed.

You need that Helmet?

Go to Froki's shack, then go up. It will be at a Talos Shrine.

That helmet can also be found inside Meridias shrine, on the ground right at the start.

Yeah, the weapon for the imps is leveled. So if you're late 20s or something, it'd be glass, etc.. The enchantment I think is random.

thanks! I did bout half of the storm cloak quest on my first play through, which, I was kinda tricked into joining. Didnt realize what I was doing and got locked into siding with them. My 2nd play through Im with the Imperials. Didnt know about any cool imperial armor, now i do. I wish there was more 'TO' this story line though, its kind of dull.

The problem is you don't get cool armor. Tullius has different armor, but you would need to side with Stormcloaks to get that. And those "elite" guards have cool armor, except my imperial legionnaire probably wouldn't join the Black Brotherhood.

Nice thing about Penitus Oculatus is you can wear their helmet with a circlet under it.