My only issue with the Atlas Mk II, like others, is the burn speed. 6, 7 with a hullmod, 9 with both, but because its a capital class those hullmods are relatively expensive: 65/220 OP iirc.
Re: Mule. I love them in the early game. In terms of combat value, they are somewhere between a combat frigate and a combat destroyer, depending on loadout. They might be "worth" 6DP instead of 7. In early game I'm no where close to having a 120 DP fleet though I don't care about combat power/DP efficiency like I do mid/late game or in a tournament because it doesn't matter yet.
Instead of a Mule, I could buy a Buffalo and a Frigate. This would be 3 fuel/LY instead of 2, probably ~8 supplies/ly instead of 7, and 350 cargo (with a mid capacity frigate like a lasher or wold) (440 with expanded cargo holds on the Buffalo if they fit with MS) instead of 250. Combat strength would be reduced, and if I need to run away (Ironmode), I'm almost certainly losing the Buffalo. Raw cargo carrying efficiency is moderately lower.
I don't particularly care about raw cargo efficiency at this stage of the game either though, because I'm usually bounty hunting: I need enough cargo to get me to my target, load up on the non-metal loot (mostly weapons), and back with spare space for emergency supplies. Mules do that for me and also give me an off destroyer.