It's somewhat ironic that the TL side had the most vocal complaints, from people who probably argued about paying huge fares and wondering what they got for their money. From day one of FCC to the end, it's clear to see just how much work has been going on.
Meanwhile, the work at King's Cross and other stations on the GN side weren't exactly tiny.
From the point of view of the GN side, I can't really complain too much about FCC.
Going back to Prism days, the trains were always been turned out in an acceptable condition, and the service generally reliable. Under Prism, the franchise suffered from driver shortages, and quite bad off-peak crowding due mainly to the practice of almost always running 4-car trains off-peak. Like other railways things got worse after the Hatfield accident.
In my view, GN improved massively under National Express, with the service becoming ultra-reliable and punctual to the point where, in my experience, you could almost set your watch by it, the trains continued to be turned out in an acceptable state, and they started a trend of off-peak trains generally getting lengthened. Under FCC this continued, with successive timetables delivering worthwhile improvements. Stations were also generally tidied up. FCC also successfully implemented the revised peak timetable, with the 321s being seamlessly integrated into the fleet, and generally the 365 fleet remaining reliable and well turned out despite being intensively worked. Compared to other London TOCs, I have always found FCC's 313s, 317s, 321s and 365s very well turned out - not perfect, but generally very acceptable. Successive timetables delivered worthwhile improvements, longer formations both peak and off-peak. This was against a background of increasing numbers of services on a very congested infrastructure, that they managed to, more-or-less, maintain timekeeping is deserving of praise. As a real-world measure of this, the service has been so punctual since the mid-2000s that I can reliably get the latest possible train to get to work, and virtually never be late.
For me, the only negatives to FCC were the widespread implementation of ticket barriers, though I think I'm right in saying this was partly DFT-led. To be fair, it has presumably reduced fare evasion. Also they did go through a period of having cancellations due to driver shortages, particularly having a nasty habit of having short-notice early-morning cancellations at weekends. But never a massive issue when compared to some issues on other TOCs. Generally where disruption has occurred (normally not the fault of FCC) it has been acceptably or even well handled.
Under Govia, I'd say things have declined perceptively. I've noticed defects with individual trains which still seem to be there next time I ride on that particular unit. Performance seems to have slipped slightly, but the worst thing is that on the (still comparatively few) occasions when the job has gone up the wall, my feeling has been that things have been badly handled. There have been a couple of evenings of disruption where station staff at King's Cross clearly had absolutely no idea what was happening with the train service.
I have no recent experience of the Thameslink side, however when I did use it regularly in the late 1990s I always found it gave the impression of a tired operation, always plagued by poorly turned-out trains and comparatively large amounts of late running. From reading posts here and elsewhere, this seems to still be the situation today. Given the obvious difference between the two operations, it's not hard to see why I'd rather keep Great Northern separate from Thameslink. I don't want to see Great Northern importing Thameslink's issues.