I think ship upgrades and enhancements should play a biigggg part in STO - otherwise you will just end up with a fleet of standard ships with no variety.
I remember one episode of TNG in particular, where Geordi La Forge was getting upset because the Chief Engineer of another Galaxy Class, made their Warp core Intermix Ratio higher than the Enterprise, so he spent hours trying to increase theirs.
This was a big subplot within that particular episode, and it always comes to mind easily.
Take another look at Voyager, all of the upgrades and stuff they had in the Delta Quadrant - Perhaps through nessesacity, but still, it stood out.
Then in Enterprise - The NX-02 had several upgrades and internal design changes compared to the NX-01.
So, 3 instances of upgrades, tweaking and enhancements in the show.....I think it easily answers the question of should it be in STO.