Since civ 4 was designed from scratch technically nothing was removed (just not implemented). Bombardment was likely not included so that collateral damage could be implemented. Far from making seige useless, this likely made seige overpowered; suicide catapults became a defacto strategy.
The flanking referred to is not the promotion but rather the ability introduced in Beyond the Sword for mounted units to damage seige units in a stack. So if you had a stack of catapults and other assorted units, and a horse archer attacked you (with a non-catapult defending), and the horse archer won (I think even if it withdrew), your catapults would be damaged. Personally I hate this mechanic, but it was part of the siege nerf in BtS (the other part was not allowing them to kill units). IMO, the latter change actually makes seige more powerful, not less, because this means that many seige units that would have died withdraw before they can get killed. The flanking promotions lie anyways, 20% withdrawl chance is only 20% if combat odds are 0% (withdrawl odds and odds to win are inversely related).
Promotions and experience are civ 4's way of making veteran units stronger than rookie units (in theory; there are factors such as free promotions, experience, etc. that complicate this).
I like how siege units are currently than how it was in Civ3. It didn't make sense to me that a bombard could miss and therefore waste the attack capability for 1 turn. Even taking over a siege unit or letting it be destroyed was a misnomer to me. Differentiating between a trebuchet and a catapult brought an interesting twist on how bombardment plays on a stack of units and a city. BTS even capped the bombard damage on SOD units which effectively limited the SOD.
Once the SOD gets to like 300 units, then its ridiculous to fight.