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Biggest problem is the drop in quality of granted patents. The system just needs a built in punishment for poor requests and the resources to sort out those poor requests. Seems that there should be a fine for patent system abuse, proportional to the abuse. That would help fund the expenses for proper screening. Also to keep the burden off of the government, we let the corporations sue each other to invalidate stupid patents, and then if found guilty the patent is revoked and the company fined ($ goes to justice system to cover court costs, the rest to the patent office.) If a company continues to get patents revoked because they're gross abusers, the fines grow quickly.
To straighten out the current system w/o all companies getting sued into oblivion, we include the option to allow companies to self-revoke their patents that are not in current contention. Probably during certain grace periods. This motivates companies to not keep a large store of probably junk patents.
Also, perhaps a bit of self regulation by bounty. Basically anyone can enter a patent and it's automatically accepted, but if someone calls you on it, you're liable for court/patent office costs if you loose and some bounty awarded to the patent bounty hunter. Otherwise the patent bounty hunter is liable for court/patent office costs for false accusations. Maybe a jury of peers would be engineers in the related field.