As far as I'm currently aware there has been one method of improving stats mentioned, via a surgical procedure. Although we don't know if it can only be done once per stat or more, it also costs money to be done.
There may also be the perks from Fallout 1 & 2 which allow you to increase a specific stat per perk once per stat and only once. Personally I think the Intense training perk which was available in Fallout 3 was a bit too much overkill.
Intense training was indeed an overkill (although, not as much as it could've been if the stats had made a bigger difference). Personally, I think increasing stats should be as rare occasion as it can get, so that one has to live with the choices one has made. That, of course, means that the stats should also be more effective for the increase to be rewarding - but Obsidian seems to have covered that, at least to a degree already. Even +2 for every stat (perks & surgeries) could potentially be too much (IMO).
Having less and less ways to permanently increase them would have an upside of making statincreasing drugs and gear much more worthwhile.