IMHO the problem with software patents is the prior art that's fundamentally attached and the degree of difficulty in discovering it. Of course, there's some other aspects:

1) In my mind, there is the disincentive to work at the US PTO [or any PTO for that matter] because the salaries suck, you're demanded to have unrealistic quota's and that means only so much time can be spent on each filing by examiners who are mostly beginning - because ones they are experienced leave to join firms who pay them a lot more because they have examined from "the other side of the table".

It's a talent glut that starts the cycle, approves poor patents, clogs the court with the attitude of "even if we are wrong [PTO] the Courts will resolve it - so we really can't make mistakes" and increases litigation costs for all involved.

2) I don't think removing patents is the solution - there have been 100's of instances where the "little guy has stopped the big guy" in all sorts of scenarios in innovation - tech or otherwise. The problem is that you have a system which is bursting because the pay cycle for PTO is low, pressure driven and this means you've inexperienced patent examiners who ultimately leave for high paying firms. Why wouldn't they ? There isn't any economic incentive to stay. Pay them more. Retain the best ones. Get better examination results, use an Open Source Prior Art system which allows community collaboration to increase prior art base and makes it harder to "prove" novelty.

3) Stopping the "patent trolls" [shell companies which no utility other than to litigate] is a completely other matter IMHO. The patent system is designed to protect innovation - I'm not sure it was designed to facilitate companies purchasing huge packets of IP protection to simply stiffle innovation. Llegislative restrictions should be placed around IP attaching to a product or service which looses it's enforceability if it abstracts itself too far from this product or service - meaning companies who acquire technology can continue to gain from their acquisition [product/service] as it is inferred they are in a similar field and therefore would satisfy any such test - but which ultimately means that trolls who acquire IP don't have anything to gain. They are too far abstracted which means their enforcability is dead.

i.e. A University developing and researching technology doesn't have an "abstract connection" to any patents they hold - they developed the technology and therefore have a direct association to the product/service - regardless of who they licence it to for further commercialization - arguably, without their initial cost of research and development the patent wouldn't exist and the world wouldn't benefit from their efforts. IF a troll acquired the patent and had no intention to develop the disclosed invention -they have no direct association and therefore it's useless. A "bad faith" test if you will.

"Trolls" - at least in my view - have no direct connection to the patentable subject matter - a so-called "abstract connection" - and therefore aren't actually "benefiting" from their effort in developing the patentable subject matter. They are essentially those entities who use patents purely as an enforceable mechanism in order to extract income from innovators and that's a sad by-product of patents unfortunately. In Trademark law, trademarks registered in "bad-faith" can be extinguished and it would not be that difficult to extend such a concept to patents such that owners who acquire patent rights in bad-faith [that is, purely to stifle innovation without any direct connection to the patentable material] - should loose them.