Good point. If midicholorians are inside your cells, then they would have to be reproducing themselves. Countless cells in your body die off each day, especially in your blood, but they are constantly being replaced (if they're not, you're in serious trouble!). So midichlorians inside your cells must also be reproducing.
One could easily argue that the midichlorians "left" inside his body just balanced things out and might be even more concentrated than before. After all, his blood doesn't need to circulate to those missing limbs anymore...
And if it were really somehow essential to have midi-blood everywhere you needed to use the Force, he could have had artificial veins circulating blood throug his cybernetic parts too (even though it wouldn't need to do anything, it would just be "there").
One theory on the "Oh, Vader is not as powerful as he could have been" thing is that perhaps you could see it this way... Yoda is an old cripple (he hobbles around with a cane), like Palpatine is. They both use the Force to "envigorate" their physical bodies so they can flip around or do other features that old men typically can't do without seriously hurting themselves. Heck, even Dooku is played by an actor who can't really do any of the heavy physical stuff you see him doing in the movie, so you might as well say he's using the Force to support his physical frame.
So if you think about the Force power available to each user (and I know this makes it sound very much like a video game but bear with me), some of this already has to be spent on keeping your body in shape, with less left over for the fancy powers and precognition for your sword fight. So a "younger" more physically fit Jedi/Sith would have an advantage in a battle with an equally power in the Force aged Jedi/Sith. Of course you could say the elder one generally would have gained more knowledge of the Force through experience, but again, they have to use more force to augment their frail body, which could otherwise be used for other things.
If we take the point of view that Vader's cybernetic parts are INFERIOR to biological counterparts, then we could say that Vader IS indeed a cripple. His cybernetic parts are inferior, and he uses the Force to "augment" them so he can do all his stuff. Without them he'd be bobbing around like C3PO. Mobile sure, but not combat worthy.
On the other hand, this doesn't quite jibe with what we've seen, because we KNOW they are capable in the SW universe of making robotic parts that are equal or even superior to biological ones (see General Grievous for the most dramatic example). Then again, perhaps that level of sophistication requires more "intrusive" surgery into the brain and spine than Vader wanted. After all he's more fleshy than Grievous and we don't see any electrodes sticking out of his head when Luke takes off his mask. So perhaps he didn't go for the extra stuff, and as a result he still had to compensate for his inferior tech in some way.
Now another possible take on this, relating to the above, may be something few agree with. I am not saying this is OBJECTIVELY RIGHT but Lucas seems to be continually promoting the idea in his movies that flesh and spirit is greater than technology. He's said that technology won't save us, he has the Kaminoeans boasting of clones being superior to droids. He makes the droids into comic relief, and he has Vader's "more machine now than man" being symptomatic of his fall and corruption. Lucas seems to view being robotic as being inferior. So perhaps in Lucas-Logic (invented a new term, woo!) the reason Vader is weaker is because he's become less "human."
He may feel that no matter how advanced, "droids" are always inferior to biologicals, so cybernetic parts are more a hindrance than a help.
In the case of Vader's death though, it's clear that the damage to his system is contributing to his death, not just the damage to his flesh. He seems to be paralyzed, implying that the robot suit was what kept him mobile below the neck. Could he have used the Force to animate his body (after all he used the Force before to keep himself alive so long on Mustafar, and both Jedi should have been killed by the heat near the start of their duel)? Perhaps, but apparently after all that fighting he just didn't have the strength anymore.
Another possible interpretation of the whole "Vader was not as powerful as he could have been" could be totally unrelated to his cybernetic suit. It could be that had he continued his career as a Jedi, rather than being so impatient, and gotten onto the Council of Masters and learned, etc (remember they said he was the youngest ever on the Council) he could have been a lot better. Instead he quit the Jedi and joined the Sith, and when the Jedi died, their teachings were effectively lost. He'd only have access to their writings (assuming he could still get to them and they weren't all destroyed) and to what Palpatine chose to reveal to him (and granting Palpy's knowledge of the Plagueis legend, he might not have felt like sharing everything, even with his trusted apprentice).
And perhaps if Anakin HAD been born in the Republic and trained from infancy he'd be even farther ahead than as things did play out.
And finally, if you believe Yoda, who says that the Dark Side is NOT stronger, then perhaps staying on the "good side" (the term "light side" comes from the EU) would mean he'd eventually become more powerful than he was as a Sith Lord.
Then again in AOTC Lucas says the Dark Side is stronger. But one could still interpret this as that the Dark Side is not stronger, but it does allow you to "shroud" the powers of unwary force sensitives, sapping their power and making them less than they normally would be. Perhaps Yoda and Obi-Wan were able to "break through" this shroud when they discovered the plot to destroy the Jedi, and this allowed them to suddenly start whooping butt on the troopers and Palpatine/Anakin, while the rest of the Jedi died like chumps from what should have been an easily thwarted attack in most cases. Anyway, that's all my speculation...