A couple of things not yet mentioned:
PLCs tend to have long life cycles, and the manufacturers typically announce end-of-life well in advance and allow lifetime-buys before ending production. They rarely stop making just one IO board...if the product series is still in production, you can still buy all the bits for your system.
When you build up your board from parts, you have dozens of parts, each of which may or may not be available the next time you want to build your boards. So you have to have an engineer on staff (I have been that guy) that figures out how to make the boards using what you can still buy. Maybe it is just a package change, or faster logic chip instead of old slow logic chip. Or maybe you can't buy the VFD display any more and have to re-write the code for an LCD display. Then the next time you build boards, the new part isn't available, but the old part has been second sourced... Also, Fox stopped making the crystal in that frequency, but ETC still has one...except the ETC rock doesn't reliably start...Oh, and you got a batch of mis-marked resistors in that aaaalmost work, and it takes you a couple of weeks before you unsolder one and measure the damned thing...yes I have seen this once with AB branded resistors.
In short, if you build boards just once every year or two, you are going to require a EE who understands the board to baby-sit each production run. Custom board/Embedded control really only makes sense for products that are in continuous production. You will still have to find replacements when components are obsoleted, but at least they generally come along one at a time, instead of the 12 that you'll have if it was 3 years since the last batch.
Low cost PLCs offer some middle ground. I've had pretty good experience with idec PLCs and panels. Automation Direct (Koyo) PLCs seem to be OK, but those little C-more displays are garbage. I think Turk has some low priced stuff, but I have no experience and have heard they are problematic. The programming tools tend to be much lower featured, and even though they use ladder logic, the ones I have used only offer basic instructions, so it is similar to assembly level programming. Still you can have a complete PLC rack for under $1K.
If you have a PC based HMI anyway, you might use a virtual PLC. TwinCAT is pretty awesome, and are some inexpensive IO options...like using AutomationDirect modules via modbus IP. But use etherCAT if you can swing it, it flat out rocks!