First of all, please know that I wrote the GSM version from my general knowledge of rooting and all of the info I could find on the GSM process. I have a CDMA version, so I can't confirm any of it by first hand knowledge. With that in mind:
1) So we need to Root the device first then back up the original stock ROM (yes I want to back it up)? or do we back it up first?
If you want a full backup (called a NAND backup, a NANDroid, or a recovery backup), yes, you need to unlock your device and install a custom recovery before you can do that.
2) By using the revolutionary method (as my HBoot is 1.49.0008), is it necessary to flash the ROM as well? By that I mean, I just want to Root my device and get rid of some stock apps and the annoying carrier starting animation. Seems to me rooting and flashing the ROM are two different things, but I would just want to make sure before I do anything...
Technically, no, you do not have to flash the stock + rooted ROM. In the GSM version of this walkthrough, I provided a link to the super user patch. The super user patch just installs SuperUser.apk, busybox, and a few other necessities to the ROM that is already on your phone. That will make it so you can debloat your phone and change the boot animations. If you ever want to branch out and do more stuff, like install themes, you should look at installing a custom ROM. It isn't that big of a deal, but I can understand your apprehension. I was similar when I started rooting, now I'm a flashing fanatic.
3) Following up the previous question, how do I get rid of the starting up animation? Is it something to do with the kernel? Or can I just do it by deleting some file?
It's really simple. Get a boot animation that fits the EVO 3D. The animation has to be 960 x 540. Look in the HTC Sensation forums and the Evo 3D forums on XDA and you should find a bunch. It doesn't matter if it's posted in a CDMA forum or not, the images work for either. They are just images ;p Then you need to find the boot animation zip files in /system/customize/resource/ and replace them with the boot animation of your choice. To do that, you'll need a root explorer app (I recommend ES File Explorer) and to mount /system as writable (done in the settings) before you can overwrite the default boot animation. Some boot animations come as a flashable zip, in which case you just flash them in recovery and no swapping needed.
4) In the case that I'm going to flash the ROM in the future, is there a way to choose between those many ROM out there? I mean, for example, the 3D camera won't work with some custom ROMs, so is there a way to know it before I flash it?
As you're on GSM, you have to be a little more careful than us CDMA users. GSM ROMs are built on a variety of carrier-flavored software, so make sure that you don't flash an Orange based ROM on a Rodgers phone (at least, I'd assume that would be bad).
Second, each ROM will post in it's OP thread the features and bug list. Make sure to read both. Then you can decide from there.
I am a newbie in rooting and flashing the ROM, and I would love to thank you all for the hard works!! I've read many post and guides in this amazing forums, it's just hard for a newbie like me to sort the information in my head clearly at this moment...
Thank you in advance for any advice and suggestions.
We were all newbies once. Start slow, get accustomed to it, and you'll be flashing ROMs and telling others how to do it before you know it.