Its probably fine to work with. Frames, like any other part, come in different qualities, weights, and levels of design. Often a cheaper frame has things going against it that doesn't make upgrades worth while, hence why past a certain price point it isn't just the parts that change but the frame and fork as well. That said, many people don't push the bike to the limits where that makes a lot of difference and there's nothing inherently wrong with upgrading a frame you like. I did the same thing with a frame for 20 years, but enough has changed that I've found it no longer holds the same sentiment it had and doesn't have the characteristics I'm looking for and I've been contemplating getting rid of it. Its you're bike and your money, want it to spend the money on it and have it be better, go for it, without a doubt better wheels and parts will make a cheaper bike a lot better, and you're the one who has to ride it.