Have had a complete play-through (finished IBB missions) with SS+/Nexerelin with this mod. The ship upgrades completely changed the balance landscape and that's what I liked most about it.
It seems that the upgrades are benefiting ships with more base flux/armor/speed stats more than those with more ordnance points, as the upgrades are in percentage bonuses (modified values in SS are computed as: (BaseValue * (1 + PercentageBonus) + FlatBonus) * MultiplierBonus). It also mixes well with ships with multiplier bonuses, like the Hegemony XIV variants, as they stack multiplicatively.
I also like the fact that the upgrades diminish the differences between ship classes. I'd found a perfect Morningstar (SRA) early on in the game, fully upgraded it and started taking it out to IBB boss battles. When I finished IBB missions it hadn't been destroyed.