Very valid points. In the first instance, it is for me only. For all that I am a self employed EE, most of the work I do is commercially sensitive, so I am tied up in a non-disclosure agreement. Unfortunately, this means that I have very little in the way of a 'portfolio' to show prospective clients - and as Dave says, there's nothing quite like taking something along to show them what you can do. This project, although a 1-off and useful to me, will be used to show my RF / power / CAD / embedded / app software design skills. At this stage, I have no intention of making them available commercially. But as it could well be useful to the amateur radio community, I will to some extent be making it open source.
The status indicator is mainly to give a go/no go indication while I am developing it, but we have seen with the Fluke 87V that even the best designed product can brick itself, so it would be useful to have an indication of problems such as checksum failure / watchdog timer overflow. The red fault indication will flash (possibly an error code) so actually being red is just an additional warning. Changing colour when actively analysing is mainly for effect, as the main user interface is via PC software. I did consider using a small LCD or OLED panel for status text, but I don't think that would add anything, merely add complexity, time and cost.
With regard to the Altera FPGA dev kit, if I were going to use it for an extended period of time, then I would increase the LED resistor values. Unfortunately, Altera have packed so much stuff onto it and made their software so complex and tied up in licensing restrictions that it is phenomenally hard to use. It is on my pile of "things to do when I have a spare week".
Mike