I've seen this idea get suggested a few times, and on one hand I like it. I truly wanted to see Toa Ahkmou. And the 08 Makuta were wasted like that.
On the other however, I would've rather seen Shadow Toa as a later group of antagonists so to flesh them out more. Possibly in a parallel world where the story focused on the MU's war against Teridax (no offense to Bara Magna fans but I just didn't care for that plot), with Ahkmou and Gavla joining as members as you mentioned.
Plus I fear that, had the 08 villains been Toa, the designers would've limited themselves to more humanoid designs, while with the Makuta they were able to get crazier.
I think a whole team of Makuta can work if you change one small detail. Of course their problem is their insane power level.
What messed everything up was the "All Makuta are on the same power level AND have all 42 Kraata powers" rule, so you got 8 Teridax-tier guys against 6+2 Toa. Of course the story team was forced to come up with bullshit ways to nerf them.
But remove that rule and allow them to vary in power, and things get a lot more even. Have Makuta range from Toa Nuva+ tier, with only a few Kraata powers at their disposal (lesser Makuta like VirginBitil) to demigod tier, with most or all Kraata powers (greater Makuta like Terry Ducks).
Alternatively, you know, keep all Makuta at the same power level and just don't make said level so fucking astronomically high. Teridax relied on brain more than power most of the times, anyway. A race of scientists never needed be so fucking strong to begin with.