I can think of a logical reason: FGM-148 Javelin. If an infantryman can take out 40 tons of MBT, I think a couple of tons of stone will go kaput pretty easy...
Ok, I jest.
But seriously, Gunpowder units as a category in Civ paint a pretty broad picture for a reason. Sure, your early Musketman might not be able to do much damage to a big hulking wall with a brown bess, but modern infantry don't just pack assault rifles.
Walls stop a bullet? Yes.
But Infantrymen haven't
just used bullets in over 300 years. They pack all sorts of bunker busting goodies. Even your earliest Sappers were often organic to, you guessed it, Infantry units. I mean, we're used to seeing modern day armies with independent Engineering units, but not all modern armies are like this. The Wehrmacht in WW2 actually operated with organic units a lot of the time for ease of C2.
And your standard Infantryman carries anti-armour weapons and explosives that would make short work of "city walls" as the ancients knew them. Remember guys, just as "Infantry" are a broadly brushed concept, so are city walls. In the game, they're on the smallest towns (If you've got Great Wall) to the largest ancient cities. They represent everything from immense towering battlements to the wooden barricades you'd find around a North American colonial settlement of the 1700s.
A bullet might not make an impression against the walls of Jericho, but Mr Carl Gustav would win pretty convincingly against the wooden walls of a Roman Barricade, and I don't think it'd be a decision on points either...
Let's not forget that ye olde IFV, representing everything from your BMP1 to your M2A3, therefore packing anything from a 70mm gun, to a 20mm-cannon-with-twin-TOW-launcher-and-a-large-coke-value-meal, is a Gunpowder unit. Still don't think a Gunpowder unit can go toe to toe with city walls?
If I can be allowed to mix my movie metaphors here - Had I been Orlando Bloom and Saladin was facing me down with a Squadron of IFVs, I'd be donning a platinum wing and some pointy ears, and running for the nearest british actor dressed in a white robe with a staff. Where's the Ring of Doom when you need it?
Without flooding the mod-devs for requests for superfluous units, I think leaving the brush with that broad stroke and killing the city wall penalty for gunpowder units is fair enough. Especially when you consider that a tough fortified medieval unit, dug in with a good defensive bonus will more or less hold it's own against an early gunpowder unit anyway, especially if the defender's got better XP.
Having said that Kirby's ideas are, as always, thoroughly worth consideration, regardless of whether I agree with them or not.
I think the inclusion of Dale's combat mod will go a long way to bringing back that well loved bombardment stuff everyone likes. For my part, I'd love lethal bombardment back again.
Good to hear that transport choppers will be back, as they really do form the only effective airborne game element, and I think the game really lacks without it. Currently, as awesome as some of the elements in TR are, I think Sevo's mod is still getting my vote simply because his mod has a chopper, this one doesn't.... Yet..
I'd like Paras too, but considering the amount of work that no doubt gets put into mods like this, I'd say other priorities are probably better for now... I've said my piece before in relation to those things, I won't say it again and bore everyone.

Needless to say I'd guess the actual coding and mechanics of implementing the Para would be kinda tough... maybe one of the resident devs can comment on this...
As big a project as it is from the feedback I've seen in this thread, I'd say the main priorities for later should remain the rebalancing of Barbs and Mercs, and the rebalancing of certain units. If this mod has an achilles heel at the moment, it's balance. And like the BF2 community like saying (and rightly so), it's more important to fix what you've got before you worry too much about adding new content.
If there is going to be some kind of Terrorist unit, I reckon make it like a ground privateer. Sure they're less likely to survive, but then regardless if you're a "terrorist" or a "freedom fighter", get stuck in the wrong neighbourhood, and you're the sh1t regardless aren't you??