This alternative is basically made up of two changes. The first is the elimination of the E6 top hat, which severely limits advancement of characters (in levels) and the second is a relaxation of the rules with regards to what magic is available.
I've been convinced for quite a long time (before I actually played through, actually, although that certainly convinced me for sure) that the d20 system derivative games don't work well at high level. They become more tedious than fun, and the math works out to some wonky results anyway. I also really dislike the obvious disparity between low level characters and high level characters; they don't feel like they should exist in the same setting somehow; heck, they don't even exist in the same genre together. Hence my adoption of E6 to keep the higher levels from ever happening.
I do, however, sometimes feel like E6 is too limiting, and I'd like to think that I could go a few higher levels. The first house rule alternate doesn't limit levels; however, it does slow down the rate at which you achieve them significantly. The new XP chart is available here. For those curious as to how and why I developed it, it's quite simple; I want to really slow down leveling and I want it to be an almost logarithmic type slowdown, i.e., I want it to get much slower the higher up in level you go. So, I took the regular 3e XP table, threw it up in Excel, and added an increasing multiplier (n) at each level in a separate column. For Level 1, the multiplier was 0... you still need 0 XP to be level 1, and that doesn't change. The multiplier n always equals the previous level's n+1. So, for level 2, the n is equal to 1, so you still go from 1st to 2nd level the same as you always did. However, to get to level 3, n=2. Rather than needing 3,000 XP to advance from 2nd to 3rd level, you need 6,000. At 4th level, n=3, so instead of needing 6,000 to advance, you need 18,000. And so on and so forth. As you can see, this means that those first few levels don't change dramatically, but rather quickly there is a very marked slowdown in how high a level you will be at any given experience point level. In fact, the XP that you need to be at 20th level in regular 3e D&D is a little shy of what you need to be at only 8th level under this new chart.
Why do I like this? Because I want to prolong the "sweet spot" of D&D as long as possible, I want to discourage high level play except for those who really want to stick with a campaign for a really long time, and I want to slow down the leveling, especially at high level, enough that I don't feel like it's an incredibly jarring genre shift when characters level on average every third or fourth session.
Realistically speaking, I'll never run a game that gets up to, much less beyond, 10th level with this XP chart. At least, not unless there's some significant changes in my own life, my own tastes, and the gamers that I game with. But psychologically, there's something different about knowing that levels are available and you could possibly get there rather than there just being a glass ceiling fiat. So, I kinda like this. Plus, it rewards those rare types of groups that keep a single campaign running for an extremely long period of time. Our own campaigns have run into a year or two in length before, but our frequency of play is not enough to make that really "count"--and of course, that's what makes the higher levels pragmatically speaking completely unavailable to my group. But still; it's nice knowing that just maybe they're an option, for when we've really exhausted the lower level possibilities for a given campaign and want to very slowly and gradually start evolving into a new genre as the game progresses.
My other big problem with D&D is the ubiquity of magic. That doesn't jive with the kinds of fantasy stories I most like, which have a dark fantasy or at least sword & sorcery vibe to them. Magic is usually scary and unnatural in those types of stories. If you're using it, you're probably paying a price for it with your body and soul. My starker rules for magic include only allowing magic to be learned via incantations, i.e., you learn one spell at a time, have to undergo a complicated ritual to actually cast the spell (so it's not really "combat magic"), and have to deal with the consequences of it, which could include ability damage, or other unpleasantness.
While I quite like these limitations, I can see how they might be a bit much for some players, so here's a more open option. If you want to learn to cast spells, you can use the rules for the d20 Modern Advanced classes, the Mage and the Acolyte.
Advanced classes are much like prestige classes in that you can't take them at first level, and they are only 10 levels in total. The prerequisites tend to be fairly low, though, so you can enter them at third level if you've targeted them as something you want to do. The prereqs are modified slightly to be that you must have three ranks of the skill Knowledge (Arcana) (taken cross class) before you can enter the Mage class, and you must have three ranks of the skill Knowledge (religion) before you can enter the Acolyte class. Other than that, the only changes you need to make are to look over the skill list and consolidate to the Pathfinder skill list that I'm using; there will be a few class skills that are now obsolete.
You can find the Mage and Acolyte here, at the Wizards of the Coast Modern SRD site. Pick the link that says Advanced Classes II and it'll give you an rtf version of those two classes, plus the some psionics classes and the slightly lower magic Occultist option (which I almost used, but I figured that if I'm going to make an alternate, I should open it up just a bit more.)
Comparing the Mage in particular to the Wizard or Sorcerer from D&D, you'll see that it comes with a faster progression of class abilities and a higher hit die. However, given the scarcity of magic in the Dark•Heritage setting and the lateness with which these characters can access it compared to D&D, I don't think it's at all unbalanced. I'm not thrilled with the fact that the Acolyte can turn undead, but since at best it's like taking a cleric level at 4th level and then going on from there, the Acolyte will never be as good as it as a full D&D cleric, and in fact, it most likely won't be worth doing very often, depending on the CR of the foes that the characters are up against. I might yet swap that out with some other ability instead, though, because I still don't like the idea of turning or rebuking in the first place. Nor do I like the concept of positive and negative energy. Metaphysically, I just can't make that make any sense whatsoever.
Incantations do still exist, so you can have access to higher level spells than those classes will ever give you, and you don't need to take either of these classes to "dabble" in magic.