It doesn't invalidate them. However, I'd like to see these games in action. We tried running a good 5 or 6 RIFTS campaigns and after having problems with all of them, we gave up entirely. I still love the RIFTS universe, but since I started playing it I've had the same recommendation to anyone running the game, "RIFTS works well if you use another system that is more balanced in order to play in the RIFTS world. Either that or you specifically restrict your players to a narrow band of RCC/OCCs. Like: You can all be humans or SDC creatures only and you can take armor, weapons, and OCCs from Mercenaries and the Main Rule Book only." Then you can have a pretty fun game because everyone is on the same level.
My guess is that the reason these unbalanced games work is because the players are put into situations where their powers don't matter at all. If the game revolves around interpersonal relationships(like the one really successful RIFTS game I've heard about did) then it doesn't matter if one player is a dragon and the other a street rat. It only matters whether one or the other can win the love of the woman they both care about.
Well, I have run or participated in 4 RIFTS campaigns that lasted at least 9 months of weekly sessions.
The 2 I ran, I used all of the sourcebooks at my disposal, plus Heroes Unlimited and other Palladium sources that worked with the Conversion manual. I did excise a couple of OCCs and RCCS- mostly because of redundancy, plus confusing or truly awful mechanics. Nothing was excised due to power discrepancy.
My players chose things from Atlantis, the Basic book, Britain and a few others. Some were inherently MDC PCs, some had MDC armor, and some didn't start off in either condition.
When it came to combat, I used standard modern mixed-force tactics. Sure a tank can directly attack infantry, but it makes more sense for a tank to concentrate fire on the opposing armor units before they take it out, and leave the infantry to engage infantry...until one side is overmatched. THEN infantry can start attacking armor directly, or armor can afford to target infantry as a primary target.
Translated to RIFTS, that means the SAMAS guys are going after the obvious threats first- the Glitterboy, the captured and converted SAMAS, the 15' tall guy who is taking on the "Walkers" by himself... The little guys had to deal with small arms fire and AP rounds, but were rarely directly targeted by things like Boom Guns...until they proved to be a threat worth targeting with one.
And little guys learned not to stand next to the big, shiny, "lightning rod" of the PC whom everyone knew was going to get lit up.
I didn't use over-the-horizon missiles or anything like that...not unless the PCs had some kind of resource that meant that they 1) warranted such targeting and 2) had some kind of potential defense.
But combat happened...at least 1 every other session.