Ultimately it would be better if the game would handle different ship tiers more gracefully. The differences between the ships are currently way too large to really do that, though, and mostly this is a problem due to the vast gains in BO powers over the tiers. You start with 3 and move up to 12, and these 12 powers are also overall stronge rthan the 3. In addition, the game seems to "nerf" powers based on ship tier as well, e.g. a Tier 5 ship using Science Team 2 heals more than a Tier 2 ship using Science Team 2. (I think it was mancom that noticed this a while back.)

These differences makes it impossible run Tier 3 and Tier 5 ships alongside effectively in an STF, Fleet Action or PvP. What easily kills a Tier 3 ship is a small bump for a Tier 5 vessel. If you wanted to use some "weights" to balance the differences, you would get ridicilious numbers that only work if everyone is playing "nicely" (for example no one is using strong AOE powers form his Tier 5 ship, and the VAs in Tier 3 ships don't start loading up Mark XI Tri-Cobalts.)

If Cryptic could fix these issues, then we might not need Tier 5 refits at all. Sure, a Tier 3 ship would still be weaker than a Tier 5 ship, but it would also not to be expected to work as effectie as a Tier 5 ship (meaning tha enemy scaling would account for the lower level, and that in PvP Arena, killing a Tier 3 vessel earns less points than killing a Tier 5 one.)