Yes, I think I have a way to make it work altogether now...
1) In the Buu Saga, I know have Gotenks as 2x stronger than Goku and Gohan at 3x stronger than Goku. This makes the suggestion that Goku might not be able to help Gohan with Buutenks much more realistic.
2) I capped Gotenks at Super Saiyan, as he should have been. When looking back, they graced the boys with far too much power. Fusion and making them 2x Goku is more than enough...
3) No need for Rosat for Gotenks. It's just not needed.
4) Goku/Vegeta are way more respected now with these changes. Super Saiyan God still puts them in their rightful place though... But it's nowhere near as bad as it was before.
5) Vegeta has Super Saiyan 3 in BOG instead of raging out. Vegeta should have Super Saiyan 3, any other point of logic is nonsense.
6) In the beginning of Battle of Gods Goku and Vegeta have progressed significantly as well. Now they have caught way up to Gotenks and Gohan, although still significantly behind. Super Saiyan 3 Goku/Vegeta are now 75% of Super Saiyan Gotenks and 50% of Ultimate Gohan. Way more reasonable.
7) Now with all of this, we can have set boosts for Fusion and Potara. The formula is now simple. Fusion takes the weaker fighters base and multiplies it by 80. Potara takes the average of the two fighters base and multiplies it by 200. Done and done.
8.) Super Saiyan God Goku >>> Super Saiyan 3 Vegetto. This still stands and the God form completely surpasses Fusion which is inline with the new thing way surpassing the old boost.
9) Super Saiyan God remains, no Super Saiyan Blue. Super Saiyan God is awesome, Blue is stupid. We don't need any more new transformations after this, except for UI probably.
10) Super Saiyan God no longer makes the user skinny. That was a dumb idea.
That's about all I have for now. Those are all great changes that makes this series way better imo.