The one good thing about the S was that as 3050 upgrades go, it actually did improve things without doing weird side-grade stuff. STK-5S, looking at you.
Not sure i'd call the Stalker 5S a sidegrade. It does spend freed mass in upgrades, just needs more cooling but that's always been the case for most Stalkers. EDIT Granted, XL engine in a slow design is questionable.
LL to LPL is an upgrade IMO, because for average pilot probably ain't capable of really hitting anything in long range bracket reliably, but up to LL mid range, LPL doesn't lose anything (gains damage) and anything closer it is actually better.
The problem with LPL comes from other options, the ERLL, PPC, ERPPC, and later Snub-nose PPC, all of which are superior in most circumstances. But in vacuum vs LL, LPL is fine. And of course there's the question of a slow short range brawler but then again, the Atlas has always been that...
Admittedly it is hyperbole to call the Atlas S model terrible, but it feels like one of those cases where others could've used these upgrades better. Contrast to the Kuritan 3050 Panther and SL-17R Shilone... In case of this Atlas, the Stalker could've arguably used the heat sinks more than the Atlas itself as FedCom designs go.
The Atlas S, compared to the D, doesn't gain much from the DHS, additional medium laser when attacking front in most cases. To be sure, it does reduce its vulnerability to external heat and eases heat management, but neither are major gains IMO.