If you opt for an older system which isn't produced anymore, it's going to be very hard for you to reach a decent collection an maintain it. Even 9v which was only recently been discontinued will be hard to find, especially straight tracks.
Also, 9V points were not automated, so if you really want automated points, you'll have to go back to 12v, which is even older and harder to get in quantities (not to mention the parts become fragile).
Rolling stock will usually be fairly compatible since the gauge has always been the same, and magnets have always been used as coupling mechanism. So there you can buy whatever you find.
And if it's for your son, keep in mind that other relatives (granparents for example) may be less informed than you and will tend to just buy whatever they find in stores. So if you go for a 9v layout but your kids receives PF tracks, he won't be too happy, much to the chagrin of the relative.
On the contrary, if you opt for plastic-only Power Function trains, even if someone manages to buy you 9v track, you can use it as is, it's fully compatible. Also, the flexible track part is easy for a kid to work with and not bother too much about whether the layout will work or not, something which can be said for older systems where you would sometimes need to draw your layout in advance to know if the geometry would make sense.
In short, I think it's easiest for a kid to just embrace the new Power Function trains, but stay clear of the two "RC" trains which weren't too good.