The idea of a part of every law attempting to explain the "intent" is really interesting. Probably hard to realize in practice, but very interesting indeed.
There are many problems with patents but the fundamental idea is not so bad. It's just that, as with everything, it can be abused, and companies in particular are prone to doing so because they are amoral (because they're not entities that can have morals!
). The problem is that companies are the main money centers of our world, and everyone wants money, including politicians, money creates influence, corporations therefore wield greater influence than people, and thus the laws shift to favor the corporation.
Anyway, there are a couple of patent system reforms I think are fairly critical.
#1: "Open source" the patent review process. Anyone can submit a patent and once submitted they have first chance at being granted one, but like any patent their application must be reviewed for prior art, uniqueness of the invention, etc. This should be judged by the population at large, not by a relatively few patent evaluators who couldn't possibly individually have the education necessary to properly evaluate evey patent. Imagine the Wikipedia model being applied to patent evaluation. 90% of patents would probably be thrown out within a week, either because there is significant prior art out there (nothing is better at finding prior art than "the crowd"), or because the invention is obvious and can be demonstrated to be so.
#2: Incentivize the *application* of patented ideas. Or, to look at it another way, discourage or penalize those who patent something and don't actually implement it in a product or service. This would address a multitude of patent-driven ills, from "patent trolls" who survive solely off litigation (contributing nothing whatsoever positive to society), to large companies who buy up patents that threaten their business model or products and just sit on them. The question of course is how to incentivize patent use. Various fee structures or "patent taxes" have been discussed which could potentially do this, and this ties in to the next point.
#3: Restructure the fees to reward single/first-time filers and increase costs for those who spam the system or are large patent holders. In other words if you have 1 patent, filing is free or cheap. If you are filing for your 5th patent, it's $1,000. Filing for you 10th? $10,000. 20th? $50,000. It's not a linear scale, it should go up quickly, perhaps even exponentially, and by the time you're looking at your 100th patent, let alone 1000th, it should give even large corporations pause to think just how valuable a given patent really is. Some might argue that there are a few highly prolific inventors who would be hurt by this, but A: many of those inventions might be invalidated if some of these other rules were in effect and B: how many of those prolific patenters actually do anything with most of thier parents? (see #3)
#4: Patent term reform. 20 years, which is the generally agreed upon standard these days due to TRIPS, WTO, etc. is just too long. The world moves too fast. 10 years would be better, but even that is questionable. The period should basically be long enough to bring the most complex possible individually patentable invention to market, and to capitalize on it for a few years at most. Personally I think anything more than 2 or 3 years of market *exclusivity* is unnecessary. If you figure the development of very complex technology may take 3 or 4 years to bring to market, and then add on 2-3 years for sales exclusivity, then perhaps 6-8 years makes more sense. I'd be OK seeing 10.
#5: Patent maintenance fees, which already exist, should be extracted yearly rather than every few years, and should also depend on the number of patents held. If you have 100 patents, your maintenance fees are higher.
#6: Life forms should not be patentable. Period. Neither should business methods or software. Anything that is subject to copyright should not also be patentable (e.g. software).
So those are my simplistic ideas. I doubt any will ever get implemented. The fee increases alone, particularly targeted at large patent holders, would help with the patent office's budget problems. Oh yes, and the patent office income should only be usable for patent office purposes.