Well, historically the Prometheus-class was considered to be a failed experiment.
In SFB, the ship has a very unorthodox movement cost, due to the reduction in size of its secondary hull; due to the way the conversion process works between SFB and FC, it ended up being more capable a ship in Federation Commander than it was in Star Fleet Battles.
Actually, one advantage of the ship in those games that isn't reflected here is the ability of the side phasers to fire "above" the flat nacelles in hemispheric arcs; in SFB and FC, the nacelles on the CA block phaser fire in the aft 60* arcs on either side of the ship (though SFB lets you fire those phasers directly aft of the ship, between the nacelles). This detail was lost with the shift from hex-based firing arcs to the 90* arcs we see in ACtA:SF.
However, the thing that really did for the class, logistically-speaking, was the need to build them in cruiser yards. The Kearsarge-class new light cruiser could be built in destroyer yards, leaving more room in the cruiser slipways for more heavy ships; making the strike cruiser impractical to field in large numbers.
Their presence in ACtA:SF is meant to show an example of the kind of one-off designs which had been transferred to the "bone yard" of the Sixth Fleet; where the Romulans were seen as less of a threat than Third Fleet's Klingon border. (This meant that when the Romulans launched their own invasion of the Federation in Y173, they ran into many of these "oddball" designs in the first waves of their assault.)
Not every ship in every fleet works out well in-universe; which is just as well, since it adds a little more flavour to the setting than simply having only ships that always happened to work out just fine for the empires operating them.