I’m not completely sure what you’re asking, and a couple points have already been addressed, however…
There is “macros” that are built into SSF4 called “LP+MP+HP” or “LK+MK+HK”, P being Punch, and K being Kick. These can be found and configured in the Button Config menu. What these macros do is activate all three Punch or Kick buttons at the same time. Ultra Combos require the input of 3 of each at the same (as you already know), and EX requires 2 of each type. Some players suggest that you learn to do EX with 2 buttons rather than the 3P/K macros so you don’t accidentally use an Ultra Combo. But, you should also know that it’s all preference and practicing will allow you to naturally get used to it.
You mention that it deters your gameplay since you can’t get Ultra Combos out, I used to do this when I first picked up SF4 Vanilla, where i’d think at one moment an Ultra would have been perfect, and I get aggravated that I didn’t do it. The best advice I can give you is to learn to never rely on an Ultra, and try your best not to focus on that. Go into Training and do Ultras 50 times on each side (to build muscle memory for both motions), you should be a little bit more consistent if you keep doing this.
Also, a good gameplay tip is to pretty much never randomly do an Ultra, it may work sometimes, but as you improve and players you face improve, this tactic won’t work. Figure out if the character you play can combo into Ultra, such as an anti-air Jab Shoryuken easily comboing into Ryu’s Ultra 1. Alot of Ultras can be combo’d in from you doing Focus Attack Dash Cancels, which means pressing the Focus Attack combination (MP+MK) at the precise moment (frame, I think) that the attack allows you to do so, and then Dash Forward (or Back depending), into said combos.
Hope that helps.
Also, I have an easier time doing alot of things on the 360 Controller Joystick than I do an Arcade Stick or D-Pad. I’ve spent a good amount of time (atleast what sounds reasonable to me) on an Arcade Stick, and I still feel more comfortable on a 360 Controller Joystick. However, i’m part of the rare cases that feels this way, and if you want to get into the Fighting scene more, then it’s highly suggested that you give controller alternatives (Arcade Sticks mainly) a try.