We all certainly have a limited budget to work with. If I had to choose, I think I would go with the H3.
When I look at the wind tunnel data on Hed's website, the Jet 90 is a wheel that has a definite sweet spot where it shines. On the other hand, the H3 does really well in all wind angles. The H3 will serve you better across a range of conditions.
The choice of a rear wheel depends on how much you want to spend and how comfortable you feel with removing the cassette to put the cover on / off. A cover will save you money, but it will cost you more time and effort to work with. If you only have 1 wheelset, it becomes a bit of a pain to keep putting it on for races and taking it off for training. Another option could be to buy an inexpensive rear wheel and adding a cover to it. You'd still save a lot of money over a disk.
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Thank you... since you have tried both would you get: the H3 of the Jet 90 if you could only have one or the other? In addition, since I only have stock wheels on my Felt B16 should I go with a wheelcover or spring for the Jet Disc?