Perceived AnomaliesFollow

Bards get track... and rogues don't?
Why not? Bards are the jack of all trades. Rogues get SoS, anyway. Ask any rogue if he'd trade SoS for tracking...

Why can't most (if not all) races start in Freeport?
It's still a human city. The evils do have to hang out in the sewers, eh?

Why are priests of discord allowed to stand around in places no other human is tolerated?
Good question. But this could be rationalized in LORE due to faction: gods extending courtesies to other gods. Plus in the early days PoD's were butt-kickers and I doubt even city guards could have taken one, certainly not solo. We used to try to one-group PoDs and it usually ended with half of us dead and the other half running to the zone!

Why can't you sail (or translocate gnome) from Freeport to any other port on Norrath? [as an example of the poor shipping routes on Norrath]
Well, even IRL carriers have their routes. Try to get a bus driver to drop you off between designated stops! There are those player-controllable boats on lakes like Rathe and Dagnor's Cauldron which you can "sail" and drop yourself off at any point on the shore. Never the easiest conveyances to manage, but a nice touch, I always thought.

Numerous classes of player-race NPC exist that you can't be (various Iksars, Erudites, etc.).
Yeah, plus I believe I've seen NPC's casting spells from different classes and also often casting the level of a spell way below their level. Sloppy coding, hard to lore-justify.

Half elves are half-human and half-elven, can worship a mixture of deities yet have far less class options.
Eh. Easy to rationalize. They're mongrels and lack the core essentials for breadth of class potential.

Why are some beastlord and Berserkers races allowed to be agnostic (when every other class for that race can't be... just seems like lazy not-coding to match lore).
Lazy coding! They should introduce a deity named Lazzeekhodah and blame him for all these things.

Mayong "ascended" why can't we roll various races that would happily live in Castle Mistmoore? Why are their deities in the game we can't worship?
Never liked Castle Mistmoore so I wouldn't want to live there. It's too creepy.

Why did they put in Froglok monks and Wood Elf beastlords if they weren't going to do the minor work of letting you select a proper home city and train there?
Blame Lazzeekhodah.

Why did they make the (atrocious in era) Twilight Sea quest drops all drop from the named (so you get 10-15 items from one kill, only 1 of which is for your class) yet never extend this courtesy to any other out of date quest in the game?
I didn't know this. Surely not all 10-15 items drop at once?

Why, for years on end, was the default "newbie" character on the creation screen and Erudite warrior (something you can't make).
Never noticed this!

Why are they so stuck on old spawn timers? Halving the spawn time in Lower Guk would have minimal impact on live servers and make the zone more challenging on Progression... one of the easiest "revamps" they could do. Taking old raid mobs on the crazy days+ timers and putting them on 2-8 hour timers would hurt what? [It's just really out of step with basically all game design since 2003...]
I wonder if spawn timer code is cross-server so this would be harder to implement than you think. Heck, I always thought it would make sense to build in variability into all spawn timers so players couldn't just set a stopwatch and await the next respawn---knowing to the instant when it will happen.