What is it about Ultras that are scrubby, or 'not about skill', as you would put it?
VS Ryu, you have to watch out for shoryus when he has 2 bars, so you have to just bait it out, then he can't ultra you outside of a focus crumple or anti-air LP shoryu.
As much as you may dislike it, a game that is interesting to watch will have a better following. Better following = more sales for Capcom. It's in their best interest to create a game that has a large following.
They've already put in a few measures against overpowering Ultras. An ultra that is combo'd into will never do 100% of its original damage; after a focus crumple, an ultra will only do 70%. They've also toned down Ultra damage from vanilla to super, and in USF4, they've noticed that Rufus' Ultra netted him too much damage, so they're nerfing the damage slightly. Actions have also been taken against Abel's ultras, Bison's U2, etc. through the series.
*Edit*
Also, they have a system in place to help the attacker. Stun.