As I've mentioned before, I've made some fairly serious changes to the Swords & Wizardry core rules for my own campaign. Naturally, I think the changes I've made are for the better; otherwise I wouldn't have made them.
However, the blindingly obvious consequence is that I've made it a bit more difficult for myself to use any 3rd-party material in conjunction with my Frankenstein-system, especially adventure modules. I have to convert clerics, for example, into my fighter-mage priests, and because I've conflated the cleric/magic-user spell lists into a 20-level hierachy, I have to refer to spell-lists from sources like Labyrinth Lord or AD&D to see just what sort of spells they're intended by the module author to have.
None of this is insuperably difficult, but it's an added burden if I want to run a module instead of building something from the ground up; it partially negates the labour-saving aspect of using somebody else's creation.
My campaign is in hiatus at the moment; we're playing through a Traveller d20-ish scenario being run by my friend Joffre. That means I have a moment to take stock and see if I want to stay the course with the changes I've made or maybe revert to a more "by-the-book" system.
I have nice shiny copies of OSRIC and Monsters of Myth winging their way towards me right now, so maybe I might shift to something AD&D-ish. I'd have to take thought to ameliorate some of the things that grate with me in AD&D, such as the compartmentalization of thief skills and that sort of thing, but it's a possibility nevertheless.