I think generally the little-guy versus big-conglomerate isn't a winnable battle; if you "level the playing field" the elephant stomps the mouse, and if you try and give the mouse a hand grenade you usually wind up giving the elephant a nuke. Thus where I'm coming from there's a background assumption that the little guy will always and everywhere be prone to get screwed, and the only sensible discussion is "how many different ways?" and "what're the systemic effects of such-and-such-policy".
Thus in that light switching to a presumption of invalidity isn't a panacea -- and has its own drawbacks, as any "solution" would have -- and is mainly addressed at mitigating the effect of junk patents, which is what your proposal is also aimed at.
In writing my response to your IBM scenario I found what seems to be one of the ways the 18-wheeler would drive through your proposal so I've put it below, before I get to explaining how the IBM scenario plays out under reduced-presumption-of-validity.
Incidentally, one area where your proposal would fail is that the IBM scenario. So you invent something novel (patentable under your regime). For this to be patentable it has to be a nonobvious combination of existing tech that's been around and commercially viable for some duration of time.
Now IBM looks at it and figures out some other components you need to actually implement it and files junk patents on those in order to force you to cross-license. IBM argues:
- the technology needed has been around for however long your proposal requires (or else your patent wouldn't hold)
- the overall product your invention enabled has been commercially viable for as long as required (or else your patent wouldn't hold)
- their patents are thus "nonobvious" (lol) combinations of preexisting technology that solve problems related to bringing to market a technology that for a long time has been commercially viable if brought to market
In theory you can patch this by tweaking the notion of commercially available or solvable to be sufficiently narrow, but in practice that's very hard language to draft in a loophole-minimized fashion; you'd think it ought to be the case that you can set up criteria that'd make it such that "mechanism for transforming lead to gold" ought to be easily recognizable as "unique" and commercially viable and "mechanism for absorbing shock from spontaneous-change-of-weight during transmutation from base metal to gold" isn't (eg: b/c it is only viable as part of a device that itself is commercially viable only due to your recent patent), but the more you start predicating your notion of "commercial viability" on "independent of any other invention" the more you undercut your likelihood of getting a patent at all.
In some ways your proposed criteria makes this worse: the kinda of stupid patents they'd look for are going to be super generic and useless (like the shock-absorber) and thus not sought after until they're needed to try and screw you out of your invention; thus their uselessness works in their favor (they won't be invented yet b/c they're so dumb) and being generic they have a pretty easy time proving commercial viability (b/c shock absorbers already have a lot of uses, and ours is better than others in some way...).
So you wind up falling back on the same-old pretty-useless nonobvious criteria to defend against IBM if they actively seek to encircle your patent with their junk. In theory they would potentially have a much smaller of junk patents laying around but without patches they'd have a much easier time rounding up junk patents once you got your non-junk patent.
OK. The validity thing plays out like this. In the IBM-threat scenario the threat is that IBM has a bunch of junk patents in technologies around whatever it is you patented, so to actually produce a product using your patent you need to get licenses from them or risk being sued into oblivion; they use the threat of that outcome to compel a cross-licensing agreement, and then run off and make the product you were going to make, leaving you in trouble.
Introducing the presumption of invalidity changes that negotiation slightly.
On the one hand, IBM's threats become a lot more empty; if you go ahead and build your device -- IBM's patents notwithstanding -- then they might well sue you but they'd have to prove their BS patents are not-BS before the trial gets very far, and if they're actually BS then they probably can't get them proven not-BS (judges self-select to take directions about stuff like "presumption" very seriously).
On the other hand say IBM goes and makes a product incorporating your invention, and leaves it up to you to go and sue them. Things here are a little less clear, which is why it's not really a panacea (but what is?). It's easy to say something like "if it's really a good patent it'd hold up in court and you'd be fine", but with any change from the status quo predicting how things actually turn out is a little tricky.
So at the margins the lone-wolf / little-guy inventor has a harder time winning an infringement suit b/c they have to prove their patent is invalid; it's thus a systemic tradeoff between far less "bite" for BS/junk patents in exchange for at the margins having some patents wind up practically unenforceable.
The compare/contrast wrt to your proposal is that your proposal leaves patents harder to get -- thereby cutting back on the BS paten threat -- but doesn't touch the strength of issued patents; the presumption of validity tweak is intended to undermine the utility of issued patents and not have too deleterious an effect on strength.
As far as validating your own patent -- if it held up in court already it's known-good. Some variants of this proposal include a notion of patents-plus (essentially, patents subject to extra scrutiny) available for patents undergoing heavier scrutiny; I'm not a fan of that for a number of reasons, but it's another option (essentially pay extra to get more research done and have your patent enjoy stronger presumed strength).
It basically trades where we are now -- too easy to get junk patents and use them to extort money from productive enterprises -- for a setup where the junk-patent-extortioneering becomes much harder, but at the expense of leaving some lone-wolf holders of valid patents less able to make use of their patents then they are under the current situation.
There are some counterbalances you can throw in -- eg, jacking up the infringement penalties => if you DO win against IBM it'll cost them a ton more money, thereby keeping the expected outcome in the same ballpark despite the reduced likelihood of the little guy winning -- but you can't get around the marginal effect of pushing some patents into the unenforceable range.
I tend to think that's probably an improvement over the current situation, but opinions can differ.