Overuse of "however" in my scientific writing? [closed]

Yes, however is fine and extremely common in scientific writing. There's nothing wrong with but either, by the way. You can also use other alternatives. For example:

Blue data is better than red data. Standard algorithms, however, are all written with red data in mind and don't work on blue data. Violet algorithms handle blue data as well as red data, but they are very slow. On the one hand, blue-only algorithms can process blue data really fast; on the other hand, most blue data is mixed with a small percentage of red data.

What is certainly true, however, is that not only is the word however used in scientific writing, it is far more common there than anywhere else. See this COCA result:

Possible fixes:

Blue data is better than red data. Standard algorithms, on the other hand, are all written with red data in mind and don't work on blue data. Violet algorithms handle blue data as well as red data, yet they are very slow. Blue-only algorithms can process blue data really fast, even though most blue data is mixed with a small percentage of red data.

Also, consider the alternatives:

Synonyms for however adv

still, nevertheless, nonetheless, notwithstanding, withal, yet, after all, all the same, anyhow, be that as it may, but, despite, for all that, howbeit, in spite of, on the other hand, per contra, though

[Sorry, Lucky, I didn't see your link at the time of editing; you were earlier]

If you start the statement with "while" or "although" once in a while, you can cut out some of the "however's".