Is a suitor's rejection due to not accepting his appearance and his mother's domineering nature considered ungratefulness for a blessing? Does this entail sin or punishment by delaying marriage? And to what extent is Istikhara acceptable in this situation?

There is no harm in rejecting the suitor for the reasons mentioned, and it is not a sin. The jurists have stated that if a woman dislikes a suitor, she has the right to annul the engagement. Ibn Qudamah said: "Nor is it disliked for her to withdraw if she dislikes the suitor, because it is a lifelong contract in which harm persists, so she has the right to be cautious for herself and to consider what is best for her."

As for negligence in prayer, it is a grave sin that necessitates sincere repentance to Allah Almighty. If you repent with a sincere repentance, then repentance erases what came before it.

Do not despair over the delay of your marriage, and have a good opinion of Allah. Allah may avert something from you and reserve something better for you, as He says: ﴿And perhaps you dislike a thing and it is good for you; and perhaps you love a thing and it is bad for you. And Allah knows while you know not.﴾ [Al-Baqarah: 216].