Even when lifted wholesale?
I know, of course, that pre-3e D&D has it's share of clones.
It's how you express/explain/write those rules, not the rules themselves.
In other words, you can't copyright the rule "Roll a d20 against a Target Number". You can however copyright the explicit explanation for how to do the process.
Honestly, you should look through the forums, because there's been an awful lot of talk over the past decade about what the OGL is, how you can use the OGL, and all sorts of arguments about copyright. At the end of the day, there's very few absolute answers you're going to get in terms of what you can and can't do; that's because IP law is complex and varies between countries.
The GSL is a whole new animal that was introduced in an attempt to prevent what happened with the d20 system under the OGL. Lots of people have been confused and thought the GSL was just a new version of the OGL. It's not. It's actually a new version of what used to be called the d20 STL; there's a large amount of similarity between those 2 licenses. WotC cancelled the d20 STL, so it no longer exists. What is there is the GSL.
The OGL is a license that WotC can't really control. It also is _not_ another way of saying "d20"; there are game systems that use the OGL but do not rely on d20 rules.
As for the whole "clone" thing... just because they're out there doesn't mean they're "legal". What people have done is produced a set of rules that they _think_ won't violate IP/Copyright; however there hasn't actually been a legal challenge to it that I'm aware of. I'm not a lawyer and I'm not aware of anyone that is a lawyer that's argued this in a court system. Unless and until it is, what you've got at best is a bunch of people that think they can do something (but don't actually have any legal background), some people that might have consulted with a lawyer somewhere who thinks it's probably ok as long as certain measures are taken, and a very few lawyers that are gamers and think it's probably ok as long as certain measures are taken but since they don't specialise in IP and the laws vary depending on the country they're not really comfortable talking about it except in broad terms.
Roughly speaking: If you want to mess around with 3.x rules, folllow the rules of the OGL.
If you have ambitions of doing 4E stuff, follow the rules of the GSL but realize that you're not going to be making a new game like Mutants&Masterminds but using the 4E rules instead; at least, you're not going to be making it and legally distributing it. Currently the rules are murky as far as homebrew stuff is concerned. The forums have folks making houserules and even some folks thinking about how to do conversions of one sort or another, but a full on "new game"? You'll likely be in violation of the GSL and depending on the scope/scale of it, you'll possibly be called on it, depending on where you post the work.
And if you have ambitions of playing some sort of legal hide-n-seek by claiming to be compatible with "The 4th edition of the world's most popular roleplaying game" to publish 4E material... well, folks have done it, but you're not going to really get enough information here on the forums to be able to pull it off.
But all this is just my opinion and observation. Sorry if it's not as helpful as it could be, but it's sort of a topic that been round and round more than a few times.