Upgrading the Warp overdrive feels bad because once you get it to the next tier, the charge speed increases significantly and you can't use the active as effeciently to farm warp. On a tier up you get 2.5X warp gain multiplier, but then you can no longer use the actives as frequently and don't get the 10x charge multiplier. so on tier up your warp gain is essentially cut in 1/4 for a bit before you gain a few more levels in the overdrive to balance it out.
Additionally, it makes it so you never want to level the Warp Overdrive unless you are actively farming warp as you cant take advantage of the charge speed. No other overdrives are like this.
The tier effects of all other overdrives is 75% or 100% of the active effect and so it always feels good to level up the overdrive. The warp overdrive tier effect does not contain any of the active effect of the overdrive.
Potential solutions: add warp charge speed to tier up effect of around 4x charge speed OR increase tier effect of warp gain to 10x. Of course that means the warp drive upgrade costs would need to be readjusted but it would make the overdrive upgrade feel better