I've had both an auto SS sedan (LS1) and a manual thunder ute (L98) and both were pretty good tbh. I drive it as a daily, in traffic every morning, lot of stop start, the manual has never bothered me, can crawl through traffic with clutch alone or drop the gears to floor it past slow drivers if needed. The auto has a bit more delay when accelerating heavy but overall I think it's a bit smoother when just cruising. I auto felt like the auto was a bit more droney with a big exhaust but that could have just been the setup on that car, the auto tended to want to try and sit about 1700-1800rpm or as low as possible when cruising, the manual I find has no drone. The auto might also feel a bit slower with the diff ratio but if you are planning to change any of that it's less of an issue. It can get more expensive if you decide to put in a big cam etc. as you also need to think about a high stall and if you get a 6L auto you might need to remove the DoD too. The auto was more fun for burnouts as just easier to do.
Overall both are good but depends what you want out of the car.
