Hi Matt,
As far as I'm concerned you just can't beat the realism of hand laid track on profile wood ties. The shot below pretty well points this out and kindly note that I have not put down any dirt or ballast, which if I do use any other than, real dirt, it will be used sparingly due to the nature of the rural back woods style of railroad I'm building.
Also note in this shot I'm using two different sizes of rail spiked down to the profile wood ties using fine rail spikes. The upper spur with the old Climax on it just starting on a down grade to the lower main line is Railcrafts [now Micro-Engineering] code 55 weathered rail as well as the closest siding on the front. The inbetween track is the main line and I used Railcraft weathered code 70 on it.
Is it slower going, you had better believe it but there are ways of speeding up the tie laying process too which I'll go into. Also by hand laying your own rail and making your own switches, you decide just how far apart the ties are spaced as well as if they're off angle a bit as well as just how evenly they are layed to either side of the rail. Also in building your own switches you can make them to custom fit area rather than being tied down to use the space required by a pre-made switch. I use a rather hap-hazard approach to lay the ties as I don't want everything to look too even and precise. After all it is a back woods line to represent a very rural era in the late 1880's or so.
I've used several methods of laying the ties, from marking the basic boundries of the ties and spreading white wood glue or yellow carpenters glue and then taking a bunch of ties and placing each one fairly quickly, as I see fit, in the glue be it dries. Another way I discovered which is a bit quicker is to use a strip of double sided carpet tape onto which the ties are stuck and hold fairly well until you get ready to use diluted white glue, usually about 2 parts water to one part of white glue plus four or five drops of dish washing detergent to act as a wetting agent in about at least a half pint of diluted glue. BUT don't be too much in a hurry to start glue things down to ensure every operates as you want and that there are not changes you might want to make.
Also when hand laying wood ties you can distress them as you wish to give them whatever degree of aging you want. I use a small wire brush to scrub over the tops to create groves and remove softer wood to increase aging. I then use one of a few stains to give them an aged weathered look.
The the beauty of going slow as it becomes almost like planning out a real railroad in that you can see various things you can incorporate as you go along. As an example I decided that an aditional spur siding on the outside in front of the Five Oaks Station would look good as well as being functional so I just need to add one more switch in the main line to accomplish that and I was planning on working on that tonight but it will have to wait till tomorrow.
Another thing you can do is hand lay the track in the areas that will be seen the easiest and use flex track in the other areas.
HTH