So basically top is always the same as side, but you can only have one of the two upgraded so have to choose. On a Vanguard upgraded side/top armour is the toughest armour in the game - even stronger than upgraded front armour - and given you mostly play anti-tank in a Vanguard it makes sense to go with the upgraded side armour. Unless you prefer nanite auto repair, which works really well with the shield.
My dream Vanguard would be side armour, maxed shield, rival chassis and fully upgraded AP cannon and Enforcer. Rolled as a gunner in similar in the past and they dominate with a halfway competent crew.
I go with the Auto Repair, Shield and a wonderful AP Titan. I have the Enforcer on top too. Funny enough these days I don't really need a secondary unless I know that the area is going to be swamped with Infantry as the Secondary has a better sight value, great for keeping watch for C4ers...
The other day I liturally took down around 20 Prowlers, one after the other with tons of lightnings mixed in all by myself. WAS FUCKING FUN. I mean I was just going around popping them then retreateing to repair then forwards again. A couple of Friends and myself in just 2 Vanguards pretty much halted a Prowler Push by ourselves, took out what seemed to be 15 Tanks and 5 Sundies in total before backup arrived. They just kept coming over the hill into our cannon fire...
When that went down I pulled my AP Lightning, still OWNED with that as well. One moment I was over extended, so I start retreating, take a hit, tap reverse and jump out, repairing as I run beside my rolling lightning, jumping back in, reverse, jump out repair while running, rinse and repeat to almost safety, then I hit a wall and lose the lightning to an ESF... Still think it looked and felt funny as hell too...