There's only so many secondary assignments.
When their first 15-20 years of mainline service ended, the more common EMD's got the call to enjoy a 2nd life for the reasons already mentioned. Superior reliability and durability, more readily available parts, a knowledge base that extended to almost anywhere in this country with steel rail, etc. GE's usually seemed to have an advantage where fuel economy was concerned though and their bulletproof 752's made them good slow speed luggers.
But it's not so much that they were poor locomotives. Railroads wouldn't of supported them en masse had that been the case. The reasons for their demise more so has to do with EMD simply being even better. Why settle for 2nd best when oftentimes, the need for EMD's in secondary services like locals or the resale market couldn't even absorb all the mainline EMD cast-offs (Like hundreds of serviceable Missouri Pacific GP18's going to scrap back in 1980 or so)? There were good reasons when they were new to buy earlier GE's (Their long-term flaws weren't clear, it spurred on innovation across the industry, delivery times, initial cost, financing, etc.), but when their day in the sun concluded, only the best had much chance of moving on to new careers and that usually meant that survivors were picked from the more numerous EMD models.
And because of GE's late entry into the market for road locomotives, they also didn't even enjoy the position that saved many an Alco. There was no inclination to purchase a GE when their product line largely was foreign to you (There's no commonality with GE's industrial diesels and outside of perhaps some of the electrical system, it's all new). But if you were a shortline running Alco's ever since you had dieselized decades earlier (And oftentimes, ran Alco's in the steam era as well), it's not difficult to imagine why you'd like to stick with Alco as later power like relatively young C420's became available at reasonable prices.
So the 1960's era Alco's lived on in significant numbers while GE's Universal series largely disappeared after 15 years or so.