1) I can't think good lore explaining wooden things m.def vs e.g. lightning or flare dart (IIRC, technically of fire "origin"). This would be just weird.
2) There's already TON of monsters with high mdef, to point its annoying and unrewarding to play as mage, ppl at most play mages as restat, not their "main" class - and use alts or restat to grind. This looks like chance to hit 2 birds with one stone, improving this aspect.
3) It would be weird if hitting woods by sword/arrows/fists is efficient. Btw logheads are OK for noobs. They DO hunt these regardless of class. At low level these are rewarding compared to many things: dont hit hard, give XP, roots are good to sell, and phy def isnt THAT bad. Ent abominations phy def is terrible. Why not? Other monsters enjoy high M.def, so why it can't happen to other classes as well? This said: it could be fun to get "task-specific" weapons, e.g. lumberjack axe, fire sword/arrows, etc - more efficeint vs "dendroids" or even setting target on fire (much like poison?)
4) As for STR: could be logical requrement for forges. So making arrow tips from ingots (or just "improve arrow" to simplify chain) should probably need decent strength. Maybe e.g. "yield per ingot" could depend on STR much like transmutation depends on M.Atk?
5) I dont see prob with monsters for different levels, its normal practice for MMORPGs. Sorry, if you come to other MMORPG, find Lv 100 boss and hit it as LV 20 noob, guess what happens next.
6) Mages can pro'lly further improve mentioned arrows making them "guided" (and expensive) by some spell. But this really needs "chaingun" to go away and shouldnt one-shot leveled ppl in PvP. Nothing wrongs if warriors help to make "extracts" or something for this process. It would also be nice if valuable ingredients are farmed/mined/hunted in dangerous corners. TMW currently lacks in this aspect, yet it can turn utterly boring stuff like mining/grinding/etc into exciting adventure. Just think you'll try "steal" resource (faster version of) Moubotaur, avoiding detection, or if this fails, few friends around can be useful! Or you die and have to travel to remote corner again, avoiding or fighting tough monsters.
7) Archers... well, in arrows supply chain they're consumer. Doesnt means they can't hunt some ingredients though.
IMO for MMORPGs its better when stylish gear also showcased in battlefield - failure to do so missing a lot of opportinities to make gameplay more interesting and basically wastes item. E.g. I can see much better use for shroom hats. How about impacting relevant shroom type spawns, for example?
9) As for low levels... there's too much things missing on low level side of things and high levelers would see no fun in low level action, so MMO part would get stuck. So IMO at least "not now" - wouldnt do TMW any good at this point, locking ppl out "most" MMO action for a while. This said: I think I invented cool way to get around this particular problem. Unfortunately, its radically different on game mechanic, expected interactions and needs really different lore set to merely get excuse on doing things that way - so it doesnt looks like one big WTF. This wouldnt fit TMW unfortunately.