Are you kidding?...there's like 4mm of penetration difference btw 1st and 2nd gun.
Stock gun: 139 mm penetration
short 88: 132 mm penetration
So the difference is not "like 4", it's 7, and that's quite substantial, if you try and penetrate tanks that have effective armor of ~120 mm, like IS-tanks, angled KV-1s etc.
DPS commonly means 'damage per second'.
If you say, stock gun does 125 DPS, short 88 220 DPS, I can only think you must be talking about 'damage per shot', commonly reffered to as 'alpha damage' in WoT.
Alpha damage is an important stat for tanks that are used to peek-a-boo, like most heavies and some mediums.
If you sit in a bush far away and hidden from the enemy, the more important stat is accuracy, aim time and damage per minute.
7,5cm L/60: Acc .35, aim time 1.7, dpm 2025
8.8cm L/56: Acc .35, aim time 1.9, dpm 1940
So the stock gun beats the short 88 in terms of penetration, aim time and damage per minute.
Also, because it's a lower caliber, shots won't negate as much of your camouflage.
If you like the second gun more, than fair enough, but please don't come in here like your opinion is the only one that matters. Especially if you haven't done the math beforehand.
You'll have problem penetrating tier 7's but the same could be said about stock gun
Using the stock gun, I had no trouble penetrating IS-1/2s, which is about the toughest thing you'll encounter, apart from british TDs. And even the long 88 will bounce on those if you don't aim for the weakspots.