One thing I would like to see is researchable engine bell modifications for the stock engines. Basically, booster, sustainer and vacuum nozzle configurations. I understand that each engine is intended for one of these three roles - I wouldn't expect the nozzle to fully change the ASL vs Vac thrust/ISP relationship to the same degree as an entire engine redesign. However, options like a lower expansion nozzle for the LV-909 could change the ISP statistics from 95/340 to 200/325, making it more useful as a sustainer engine but sacrificing efficiency in Vacuum. The LV-T45 currently has 270/320 - a booster configuration could change it to 285/305 for better performance on the pad. Essentially, give engines the choice of two of the three types with each having a unique balance of performance.
Many real engines have this type of customizability, and it was common in the past when only a small number of reliable large engine designs had matured. It would be nice to see this element from RO added to the stock game.