I built a system for this and it seems to have been quite successful.
First, our group has been playing 40k RPG of various forms since Dark Heresy first game out, and we play all 5 game lines (everyone has the stuff for Only War, we just haven't started an Only War game yet, but several are in the works). When Black Crusade first came out, I started building characters in it to see how they stacked up with other game lines and was rather disappointed. Each time the mechanics have been updated (DH to RT, RT to DW, DW to BC), we've imported the stuff from the new system that we liked (which was generally most of the mechanics). Unforfunately, the xp costs for everything seem to have crept up to ridiculously high levels (highlighted by the fact that we have characters from DH that are at high ascension level, rank 14-17 now).
In DH, things that your class was supposed to be good at were generally 100xp. In RT, classes are far more of a straightjacket than they were since there are no branches to the paths, plus talents that you should have by Rank 8 as say, a guardsman, are held back until Rank 12 as an Arch-Militant. It got even worse in DW with things that you're supposed to have being even more costly than RT, and marines having to wait until Rank 16 for certian talents that Guardsmen got by rank 8-10 (I'm going by universal rank here, not the renamed ranks with the same totals from DW).
Since everyone wanted characters balanced against their existing Dark Heresy characters (of which we have a spread ranging from rank 3 to rank 17 with about 6 different acolyte cells), I started making a priority system for adjusting costs that was eerily similar to what was released in Only War. Once Only War came out, I mercilessly looted it for ideas for my freeform system and never looked back.
The basis is thus. You choose affinities not unlike Only War (although since things have been so freeform, the selection for backgrounds is starting to resemble GURPS). We've experimented a bit, but have settled on 8 affinities for a character. Each skill, stat, and talent has 3 affinities listed next to it. For each matching affinity, it lowers the cost by one step. Additionally, a significant number of them have a chaos affinity attached to them that can also reduce the cost by a step, sometimes two. Every advance has a cost number next to it on a big spreadsheet.
To simulate how some things increase cost each time you buy them, stat buys go up on the chart by two steps each time you buy one, but are open ended so you can buy as many stat advances as you like. Openendedness is a deliberate feature here. Skills go up in price each time you buy them, and some talents like Psy Rating and Sound Constitution go up each time you buy them as well.
The main cost tree is a 10-step pattern of 100, 125, 150, 200, 250, 300, 400, 500, 650, 800, then starting again at 10x the cost of the previous (1000, 1250, 1500, 2000, etc). This way things eventually become prohibitively expensive but are never barred from purchase. I also have a bunch of new talents that we've hatched as various character concepts have suggested - improving suppressive fire, ability to assess a battlefield more quickly, variations of the ascension talents that make more sense, ability to dip into Deathwatch squad abilities, etc.
If anyone is interested, I have a spreadsheet for it.
Edit: One other important change - acts of devotion. Buying advances aligned to a particular god does nothing. Committing acts that please a particular god are what aligns you to a particular god. As it currently stands, there is no incentive for a Slaaneshi character to indulge in acts of depravity, as that will only gain corruption, thus shortening the character's life for no benefit. If such acts count toward becoming aligned and getting a free mark, then there's a reason to want to carry out these things. Once you become aligned, you get rebated the xp spent on aligned advances (I no longer have opposed advances either, that proved unnecessary when your actions became what mattered). This actually seems to have strongly encouraged unaligned characters to pay homage to the different powers carefully (much more difficult than just selecting advances that don't tip you) and for aligned characters to continually make sacrifices to their chosen power (since you lose an act after every chapter of the story, forcing you to keep up your devotions continually).