Your argument that pitchers look ridiculous batting/running the bases is baseless. They don't have to perform poorly and teams don't have to draft/sign them. If they abolished the DH that would stop that crap right there. Colleges would then have their pitchers bat, which is what they should do since they are out on the field. Every team would have the same advantage/disadvantage.
In the past most shortstops didn't have very high batting averages. Most teams didn't weigh that part of their games as much as other positions because of their "highly specialized skills and talents". It's time we did away with this fallacy that pitchers can't bat or run. Good god, they've got two arms, two legs and are supposed to be athletes. If they can't then maybe they need to draft/sign someone who can. I see examples every year of pitchers that successfully lay down a bunt, hit the sacrifice fly, make the shallow single or steal the base. Baseball should evolve like you say it has. It's a blight on the game and should be remedied by abolishing it in the AL.
Yep...completely baseless.

That, my friend, is what I call a "blight on the game".
By your logic, you'd require kickers to play WR or RB. They are football players, they have two arms and two legs, and are supposed to be athletes. No...nothing would suffer at all. Great WR's would simply learn to be great kickers in their spare time. Sure, DPE might pull a hammy and be out for the year while kicking a meaningless extra point in a blowout victory, but apparently that's perfectly OK for you.
Colon has no business being in the batters box or on the base paths. Why do you even want to pay to see that? Why do you want to see good pitchers lost for the year doing stuff their bodies weren't trained (or even designed) to do? Just because some good things happen every now and then with pitchers at the plate doesn't mean that is (or even can be) the norm. It isn't, and won't ever be.
You seem to be under the impression that guys that throw 95 and hit .280 (or even .200) at the MLB level are just out there waiting at home for the call from a club. Neither one of those things is that easy by themselves, let alone being able to do both. Each one is kind of a full time job that involves very different mechanics, body make-up, and skills.
The simple fact that Colon
is out there
on an NL team completely tears apart your "they don't have to sign them" stance. They don't have to sign him, yet they did anyway (for 20 mil over two years). Teams will always sign the best pitchers they can (even in the NL) regardless of his hitting and base running acumen. In other words, they voluntarily gave up 3 outs every 5 days just to get him on the mound. Clubs (obviously) don't give a crap about whether they can bunt or hit a sac fly. They need outs.
Colon is perhaps the worst hitter in the game today. They had every opportunity to sign a guy that was a better athlete and hitter, but they didn't. They chose him instead because he's a good pitcher, which is the job he was born and trained to do.
All that being said, I'd still go for abolishing the DH if it meant that both the NL and AL would be on the same page. The fact that half of the teams in the same league play by different rules is literally unheard of in any sport that I know of. That is a bigger embarrassment than having to watch Colon at the plate.