I am amazed that this issue is still not resolved or will probably not be resolved after 5.0, if ever!
Weapon upgrades should be improving the weapon, not making it less useful or more unpredictable to use in a way that can backfire where it hurts the most.
Yes, I am talking about useless weapon upgrades, like Frog transformations, create a (color) Gem, create a Doom skull, etc.
One perfect example is when I had a a perfect 4 or 5+ (explosive) skull match, but then the weapon upgrade actually decided to interrupt or disrupt the perfect link with a useless color gem that made me miss my turn, gave enemy all the skulls and extra turns and costed me a win in Guild Wars or PvP. You get the initial idea and you were reminded about it a lot in the past.
Please, make all the weapons equally or more efficient after fully upgraded, but never less!