A built-in processor with Linux, running the mining software and a web server for configuration, making it a completely standalone, plug and play device, would be highly desirable. As you mentioned before, this adds time and risk to the design. We can in-depth analyze adding it in first design, or maybe in the future.
Adding full standalone capability would involve additional hardware on the main board. Some flash memory (perhaps a micro-SD card interface for convenient upgrades), a cheap LCD display for status, an ethernet and/or wifi controller, and probably replace the proposed FTDI chip with full USB host mode support since there are already existing Linux drivers for this. This increases the cost of the hardware, though not by much, and it increases the complexity of the hardware design, which increases the development cost and time required somewhat. I like the idea, though I wonder if the priority should be this level of functionality versus just getting something out there ASAP. Also, if we go with a soft processor with MMU capability (like NIOS II), that will involve some additional outlays in the form of IP licensing fees.
Intermediate steps are possible as well. With a decent design, it should be possible to fabricate the ASIC in such a way that a later revision of the board can contain a cheap 32-bit ARM processor on it running Linux that allows the system to operate standalone (e.g. run something like cgminer locally). Providing for a daughterboard to be connected to the original board adding this functionality is another option. This may allow us to finish an initial design a month or more earlier while leaving the door open to future expansion.
In my mind, the priority should be getting something working finished as quickly as possible given the volatility of the market and the potential to have other people in this space in the future as well. Wouldn't being the first on the scene with this type of hardware convey a significant business advantage over competitors absent some compelling performance advantage? Based on the Altera-provided timeline I posted the URL for a few posts ago, it seems that my earlier six-month estimate may even have been overly conservative, and that a four months may be doable if the funds can be raised.