I love this contribution, it has essentially allowed our store to use product options where due to the tedium with the default system we would not have had the patience to use product options. However, as others have mentioned a few modifications would be great.
1) (as mentioned, a lot) A sort order field would be immensely worthwhile. Currently I am using the sort order contribution #1822 in junction with the Ajax attribute manager. While effective, it's exceptionally tedious going through a page refresh on every single product option sort order. If possible to combine the Ajax Attribute Manager with the Product Attribute Sort Order I feel this contribution would be almost perfect.
2) (also as mentioned) The template system is awesome. However, it can be a bit tedious again going through each item and adjusting the price. Currently making a product option price change across many products is still tedious. If a change could be made, then saved as a template, then loaded on each product page the work required to update options would be minimalistic.
3) If possible, incorporate the ability to change how the options are displayed (ie drop-down, radial button, check boxes, etc).
4) Images. Another contribution (#1467) appears to allow the use of images next to each option. The usefullness of this contrib should be apparant and would make for the cherry on the cake if incorporated with the Ajax Attribute Manager contrib.
As this contrib appears to still be in Beta since march, I can only assume the above suggestions have already been taken into consideration. If not, then please do :) I anxiously await the next release of this awesome contribution.