I prefer to handlay track because
1) I can suit it to the era I'm modeling. Even the best looking flex track (ME) looks like fairly modern, main line practice. If you are modeling an era that didn't use sawn and cresoted ties, large tie plates, full ballast, 7"x9"x9' ties, etc, you are forced into hand laying by default (or accept a less accurate appearance). That said, it's quite time consuming to model all those details, including 4 spikes per tie. So if you are modeling main line practice of 1930s or later, the ME flex track rivals anything you can do handlaid. But remember, that doing a nice job of laying and weathering commercial track is also time consuming.
2) the order of events better simulates prototype track laying. I can put my Homasote roadbed in place, then fill in all the scenery I want (as long as I don't interfere with access) before laying any track. I can then add ties, sand them, and paint or stain them to the exact colors I want without any rail or ballast in the way. Sanding the tie tops guarantees the level surface for my rail. Sanding cork roadbed before laying flex track to get rid of vertical irregularities is recommended, but few actually do it. When I'm ready I add ballast - I put that in before I lay any rail (just like the prototype), and it's much easier to do at this stage. I also paint the rail before I spike it in place - again much easier to do, and I don't get it on the ballast or ties unless I want to. Feeders are soldered onto the rails, and the rail pre-curved before spiking it down (I use a rail bender for this now). So when I have spiked my rail in place, the track is complete, weathered, and ready to use - sort of like driving a "golden spike" for each section.
3) the track "flows". You can't find the joints between my turnouts and the rest of the track because there usually aren't any. The rail is continuous right through the stock rails of a turnout. In all but the best laid flex track and commercial turnouts, the joints are easily spotted by the missing ties or changes in ties spacing and the out of scale rail joiners.
4) increased reliability/fewer derailments from the track. Very few commercial turnouts are completely to NMRA spec from the factory. On the other hand, you take the time to get handlaid track right from the very start. Most commercial flex track tends to be on the wide side of gauge tolerance which accentuates the "wallowing" problems of some steam locos. I can lay my track to be on the narrow spec to reduce the wallowing. This also allows me to more easily run the narrower and better-looking code 88 wheels in HO.
5) pride factor. Watching a train flawlessly and smoothly run over track and turnouts you built is an ego boost. The untold secret is that virtually anybody can build reliable handlaid track - it doesn't take as much skill as it appears.
6) I can easily suit the level of track detail to my tastes and time available. If I want to just spike every 5th tie instead of every tie, my track will be just as reliable. If I want to add tie plates to every tie, or just some of them, I can do that. If I want to use grape vine twigs to simulate hewn ties instead of sawn ties, I can do that. I can choose the rail size I want without worrying about turnout availability. If I want to use a simple PC bar turnout throw, I can do that. Or I can choose to use accurate model switch tie rods and an under-ballast throw bar. And I can vary the level of detail according to how visible the track is. If I like the looks of a stub turnout instead of the point variety, I can choose to do that, too.
Remember, track can be a model, too.
my thoughts, your choices