Both have their uses imo, I prefer moss on tools i don't use too often, and flux on the ones I use more consistantly. Stonebound/Jagged/Slimy tools, i generally prefer Flux on however, as moss counteracts the boost from the material.
An example for me is my Pickaxe usually has moss, but my hammer will have Flux.
I like moss for early game tools, usually steel, that I don't want to invest a lot of other resources in. I like rf on my better set of tools, especially in combination with some form of power armor that can charge them on the go. Moss is easier to get with fewer resources, but repair is slow to moderately slow depending on how many you add. RF can be recharged faster but needs a power infrastructure in place.
I like to use moss on things like shovels and axes and swords which don't get really heavy use. I use flux on pickaxes and hammers. The only exception is early on i use moss on my pick before i get a good power setup going.
I personally use mossy. I find that by the time I've gone far enough to have advanced tools that are worth putting Flux on and having to charge, I've usually got a semi-automated mining system.
Early game I go for mossy, make the mining bags, and once the tools get close to breaking I just go and work on infrastructure and other things until they're repaired enough for another mining expedition.
I usually find that by the time I hit the 5 hour mark I've got some kind of mining system in place so I don't have to worry about my tools breaking.
Depending on modpack/configs, Moss is easy to get early game and is usually best when first starting (Stone into a Chisel to make Mossy Bricks then 9 Mossy Bricks in a crafting table for Moss.)
However Moss is far too slow, even with more than one level.
Flux is the best for all things and works best with Stonebound/Jagged but you still need a half-decent way to generate and store lots of RF for it to be effective, at least if you go caving/strip mining a lot.
First set of tools I make (Stone or Iron head) I usually go with 2 or 3 moss and avoid everything else, unless I want a diamond on the pick.
I still repair manually after heavy use but after casual use it can repair itself. When AFKing (waiting for early game ore processing), I choose to wait underneath a glass roof in my base, to get the improved repair rate.
Once I make Steel or Cobalt tools then I go for Flux, while going for the highest capacity I can afford.
TLDR - Moss for early game tools. Flux for anything past Steel tools.
Early game I use stone tools and make sure to carry a crafting station for quick repairs. Its easy to get a supercharged stone tool with fortune 3 and everything. Later on, I always set up an auto-recharge station for my flux tools. Drop into black ender pouch, through energetic infuser and into white pouch. Wireless chargers are only for the worst kinds of people.
Auto-Repair (Mossy) is slow. And even slower when not in sunlight.
So I use mossy on my sword, shovel and axe as these are tools I only use for a short period each time and then they have a long wait in between uses.
So they have time to auto-repair.
But the the pickaxe is usually heavily used for longer mining turns and always underground (no sunlight),
so I use flux on my pickaxe and have at least a hardened energy cell flux capacitor or better with me, to reload it constantly.
Have to say I'm one for Mossy on my Late-game tools.
My set usually consists of:
Broadsword: Handle = Alumite Tool Rod, Guard = Paper Wide Guard, Blade = Manyullyn Sword Blade. 6 Modifiers (Netherstar + One Diamond and One Gold Block and the extra modifier supplied by the Paper Wide Guard = 6 Mods.) Full Luck, Mossy, Save 4 modifiers for hammering on with Quartz for Sharpness bringing the Blade up to a staggering 21+ Attack Damage, capable of easily one shotting.
Pickaxe: Handle = Manyullyn Tool Rod, Binding = Paper Binding, PickHead = Manyullyn Pickaxe Head. 6 Modifiers, Full Luck, Mossy, Save 4 for Haste (Redstone.)
Shovel: Handle = Cobalt Tool Rod, ShovHead = Cobalt Shovel Head. 5 Modifiers, Mossy, Save 4 for Haste.
Hatchet: Handle = Cobalt Tool Rod, HatchHead = Cobalt Hatchet Head. 5 Modifiers, Mossy, Save 4 for Haste.
Hammer: Handle = Tough Manyullyn Tool Rod, Plate 1 = Cobalt Large Plate, Plate 2 = Ardite Large Plate, Hammer Head = Paper Hammer Head. 6 Modifiers, Diamond, Silk-touch (Silky gem,) Mossy, Save 3 for Haste.
In all of this, the only thing that would ever catch out my eye would be the Hammer, why a Paper Hammer Head you ask? Because it's easy to repair if Mossy ain't cutting it, Simply smack on down a Tool Station and apply a couple Paper Stacks to the Hammer and you're rolling. The base Durability for the entire Hammer is 10k+ so it's ideal for me entirely. A cheap ore-grinder.
In all honesty though, Flux has it's advantages, I know you can wirelessly charge the tools and this keeps attracting my attention and making me want Flux so much more now... Both are pretty good really, but in the end I'd say: