I know there are a ton of ideas floating out there, but still I'd like to share what I've thought of (for some time now) on my own. The simplest answer, as I agree with a lot of others here, is that walls/castle should provide some defensive bonus that cannot be bombarded away. Ideally I'd like cultural defense to have this too (in fact, it makes no sense as it is now - cultural defense is the people's willingness to defend their city and homeland - how can you bombard that away?) So what I'd do is first make walls and castle add their bonus on top of culture (reduce them from 50 and 100 though, subject to balance). Then, the siege units of each era have a limit on how much they can bombard, something like:
catapults/trebs can bombard walls to 50% of original, culture 50%
cannons/frigates bombard walls to 25% of original, culture 33%
artillery/modern tech bombard all the way, culture 25%
This would also be subject to balance of course.
However, there is also a need for attacking to still be viable - hence I would like to introduce a new mechanic for capturing cities. First, a city which has starved/is starving is subject to a chance of revolt (and hence surrender). Then, as with naval units, attacking enemy units exert a zone of control preventing the tiles in the 3x3 around them from being worked by the city. So a few attackers can starve out a city if the defenders don't sally out, even while taking the walls would be much harder. The spy incite revolt mission should probably also be made more expensive or changed.
Also, I'd really love for siege units to simply have a ranged bombard ability (does more damage/collateral with promos) as their main attack - no attacking with collateral damage despite that being the "thing" of civIV. This would make it possible to soften up the top couple of defenders if you brought a strong enough attack force along (also prevent a couple of defenders from holding a city against an obviously superior force- also keep them trapped in the city so they can't break off your seige.
Edit: Heh, page 3 is where some of the real discussion is at! Like I've agreed not obsoleting them is of course sensible - at least not until things like bombers. I don't think a "lockdown" mode is a great idea for civ though - letting the attacker starve the city makes more sense to me. Lastly, a point discussed about garrisons relates to another idea of mine, something I was just talking about in another thread - I think that units with city garrison promos should be able to garrison for 0 upkeep, while unit upkeep is increased for all other units (this also would allow cool things like entirely eliminating inflation, IMHO - you could have late game tech units like tanks cost like 5 gpt but at least you have an honest choice on what to do with your money.) Walls and castles and barracks would increase the number of units you could garrison in a city.
Not trying to overly tout my own ideas, but here's a link anyway (near the end):