I should first make the disclaimer that I'm a product designer, so all of my responses are tainted by that fact.
None of what would typically be considered "shortcomings" of the Elise bother me at all. These include the lack of amenities and occupant comfort issues. I don't even mind the paint imperfections (after I buffed them out), grit under the Star Shield (I'll ignore that), rough engine idle and performance when cold (kinda like the sound that it makes), water leaks around the windows, and marginal air conditioning. In my opinion this gives the Elise a real sense of character that is sorely missing in todays "santitized for your protection" mass produced cars. My point is, don't add or refine things to try and make the Elise acceptable to the general public. This isn't a generic car and Lotus should never attempt to make it one. My one suggestion for the current list of options is to make the car standard without a stereo, and make an optional stereo of higher quality for those who want it.
The main issue that bothers me about the Elise is the styling. It's not that the current styling is that bad, its just that Lotus doesn't seem to have any brand identity in its product line. Comare the current product line of the Elise and the Esprit to see a good example of a lack of brand identity. The original Elise was definitely paying homage to the Europa in its facia, but the overall styling was a bit too retro and cute. The S2 followed the styling cues of the 340R very well but was a bit too swoopy and overdone. The next generation Lotus appears to be going too far the other way to the conservative side. Perhaps the design department within Lotus should have a bit stronger position in the company with more of a long-range strategy than they currently have. The proper evolution of design makes for a strong visual brand equity.
John