Leaks and pad height aside I think you'll find its pretty much all technique - so thats embouchure and mostly diaphragm breath support. Middle D and Eb require more support than most other notes and you'll also find that middle B, C and C# can sound brash/harsh and so need perhaps a little more control in the opposite way. Also lower notes C# C, B and Bb require more support whilst upper notes from C#/D upwards meed extra oomph and a strong embouchure if they re not to sound thin. Then there's he middle G/G# squeak/warble that plagues us from time to time!
There's a great book by Larry Teal The Art of Saxophone Playing that you should find helpful and at less than £8 it's a bargain. Also most of the top players use Top Tones for the Saxophone by Sigurd M. Rascher which has some excellent advice and exercises on solving this issue and on evening out the sound across the whole register. At less than a tenor it's a great buy also.
It's taken me almost 3 years to master this and even now I lose it around the same troublesome notes occasionally. Good luck!