So, lets talk about modules.
Dreadnought "Armor Amplifier IV" vs "Armor Amplifier V": AA-IV is a good solid ability. 10 seconds of 90% damage reduction. Commonly coupled with "Slow and Steady" briefing for 100%. AA-V, on the other hand, is 99% for 5 seconds. Anyone blindly upgrading their T5 Dread modules might overlook this, and be sorely disappointed at the discovery. The situation only gets worse when they realize that they can't use AA-IV anymore since they've got AA-V. I'd like to see AA-V get re-evaluated. In it's present state, it will likely never be purchased with informed intent.
Artillery "Rapid Fire III" vs "Rapid Fire IV, V": Similar situation. RF-III is gud. RF>III is not gud in comparison. 60% rate of fire increase for 6 seconds VS 75% increase for 4 seconds, PLUS stops movement and drains energy. Again, no one will purchase this if they realize what they are getting into, and anyone who does will be disappointed they can't use RF-III anymore.
I'm sure there are more modules like this, but these are the two I know of.