True, but not every class is suited to node defending and balancing to account for 1v1s with all classes would be a disaster. Node defending requires the classes that are best suited to it (mara, op, sin, sniper arguably, potentially others). PvP as a whole means that this cannot determine balance, you just have to roll with it.
PT burst is significantly stronger than marauders and cannot be countered well outside of a long cc. Can't be interupted (like ravage), cleansed well (like annilihation) or kited well (like rage). They do drop quickly when focused which is exactly as it should be, they are a class cannon, burst balanced by lower survival.
Note that UD is a defensive cooldown, of course they're going to be better off if they use it, what would be the point otherwise? Other classes have access to other defensives, but the nature of those defensives mean they should be used at a different time. UD just before death, most others just before damage is taken (clever applications aside).
I agree with your point about not focusing marauders first. This is perfectly fine as they can be countered well enough to avoid needing to be focused immediately. A good team will notice when the cooldowns are used and focus then if need be.
I would not say VG burst is significantly stronger than sent, seeing as how a sweep bomb into a group of people is harder to heal through than just one person getting nuked. You're right that VGs are glass cannons, and guess what the best counter to a glass cannon is? Kill them first. That doesn't work with sents, and chain CCing them doesn't quite work if their team has good healers that know what cleanse is.
I agree with you the game shouldn't be balanced SOLELY around 1v1s, but it should be balanced around it partially. I'm fine with having a LoL type (rock, paper, scissor) balance for 1v1s, but currently it's rock, paper, scissor, HULKSMASH, where sent, vgs, shadows are the HULKSMASH that own everyone else. That's not ok.
In WoW (the only other MMO I've played seriously), every class had a good chance to beat most other classes, and get utterly owned by some (or at least manage to stalemate). And they still managed to balance the overall larger scale pvp quite well.