Who exactly was the masochist who thought that tuning some notes slightly sharp and others horribly flat was a ‘good’ idea?
I’ve had some people try to justify it, but wtf - couldn’t we just poke the proper holes in the damn thing instead of making players lip every note a different way?
You might just as well ask what masochist thought equal temperament was a good idea. 
Now that I’ve got that off my chest. . . There are some things that must be built into a tenor flute in order for it to fit human hands. The simple-system flute necessarily can’t be made “perfect” in both pitch and volume for every note. The note that probably bugs you the most is the C# – there are two things that affect it. One is that on keyed flutes, it’s generally designed to be in-tune with the C key vented, the other that many keyless flutes are optimized for the Cnat to be in-tune. Either of these will make the C# flat. Similarly, on baroque flutes the F# is often flat to allow the Fnat to be more in-tune. Some makers favor a stronger E note, which will make it sharp, others favor an in-tune E which sounds somewhat veiled. Some, though are able to work magic and make a strong E (and A) that’s perfectly in-tune for most players.
But even within those limitations, the flute is a very flexible instrument, and a good player can make the notes sound the way he wants them to. Chris Norman once said to me, “Don’t blame the flute for your inability to play it in tune.”
The flute is just a damn hard instrument to play in tune (probably true of all wind instruments). Nearly every player from the lowly to the greats play out of tune at times. Drives me crazy too. Just have to fight on.
Behold, the proper hole arrangement of the 12-hole flute:
Here’s a thought: I reckon if you’re playing the As and Bs sharp and the bottom D flat, then maybe you’re also playing the As and Bs too loud and too screechy, and the bottom D not hard enough and with insufficient tone.
Some older thread, (I’m too lazy to search), talked about how each of the notes on a simple-system flute really has a personality of it’s own. Each has just slightly different breath requirements, and responds just slightly differently to all of the physical factors involved in playing the flute. This is largely what gives the ‘Irish’ flute it’s unique, warm and life-like personality.
The Boehm system, despite its many technical advantages, is a very different beast. There are good reasons why only rarely are they well-presented in traditional music (from any nation).
bit new for many of the traditions, aren’t they?
Yes, my point being that they rarely find their way in, as their technical advantages come at a cost.