Full server wipe would only last as long as it takes for the organised groups to earn back their caps. It's not a sustainable solution. Knjaz is right: the main reason why bases are so hard to kill is to prevent 3 AM base rapes and the resultant griefing.
I would say there needs to be a different way to rebalance bases, one that allows a sustainable base but also one that means a base is destructible if you go after its profit and suppliers. Furthermore, offensive bases should be harder to maintain than trade hubs (easily explainable in RP).
Here's a list of changes that I would do to bases:
1. Make defense platform respawn take a small amount of resources from the base, increase respawn times. This will allow an offensive base to be "raided", which will be a good offset to the power that it projects across an area. An offensive base like this will be a bigger money sink than a normal one, especially one with a lot of turrets - the more turrets there are, the faster the resources will drain during a sustained siege.
2. Make it so that base commodity sale price can be different to the buy price. This will allow trading bases to be less reliant on micromanagement and buy/sale time curves. It will allow people to more easily create an "economic eco system" whereas bases will be established for aggregation of commodities then resell at higher price. It will be like a free market system where the best buyer/seller wins. For the purposes of trading posts this will be fine.
3. Finally, there was a proposal somewhere about base "tech trees", where you would choose a base specialisation and according to that you'd be able to build it up in a specific way. The ideas were roughly: trading post (focus on storage), science centre (focus on factories), military outpost (focus on defence). A specialisation would place varying limits on the amounts of modules you could construct. It could also provide different benefits like varying numbers of base HP, varying entry storage and varying module costs. All in all it would ensure that you need a substantially greater amount of work to for example manage an area lock down but also successfully run a trade facility out of the same base. It will ensure that even factions who have bases will still strive for cooperation with other base owners, perhaps creating things like confederations.
Those are my relatively short and fairly doable ideas. I'd welcome people to build on them.
