Photoshop is the only program I've ever used and ever will use. I started with it because of a disc that came with a printer my parents bought when I was in middle school, and I continued with it because it's industry standard (if you ever decided to work professionally for a company, photoshop is what they'd make you use, so knowing the program is important, but only if you wanted an on-site job somewhere).
Currently you can actually get a subscription for photoshop that's only $10 a month (which considering it used to be thousands of dollars to buy the base and sometimes even the upgrades, is an incredible good deal. A lot of people in general seem to be unaware of this subscription service, though). I know some people have complained in the past about brush quality and versatility, but they've honestly improved 'em over time, and especially coupled with a decent tablet, feel amazingly good to use. Oh yeah, and I will point out that what tablet you have does matter when it comes to using programs like photoshop where the quality of your line isn't artificially adjusted to make 'em smoother at all (This is why you'll see a lot of artists use multiple programs, one for inking, one for painting, etc). A lot of other programs will adjust your lines subtly to help get around any hardware limitations, so you may be better off using a program that does this subtle adjustment if you're looking for something to do all your work in (I'm not familiar enough with Manga studio to know if it does or not, but I know SAI does). There IS a tool to do this in photoshop called Lazy Nezumi, but it's a mod by a third party you have to purchase extra for about $10 (I think. It's been awhile since I looked into it). It's not all the mod does, as it's got a huuuuge variety of other handy tools (like adjustable perspective grids and the like). If you have really shaky hands, Lazy Nezumi is a life saver from what I've heard. I played with a trial of it a little and considered getting it, but haven't yet.
I'd honestly just recommend looking at free trials of several programs and seeing which you like best, cuz in the end, it's going to be a matter of preference. MOST painting programs have 30-day or limited trials you can pick up, if they're not just straight up free. Cuz I've had people tell me in the past that such-in-such program was really easy, and then I'd open it up and be baffled as to what I'm looking at. (annnnnd I know Photoshop can be one of those confusing programs for people, because it is a little overstuffed with tools)
If you did end up deciding to use photoshop, I highly recommend getting some of Kyle T Webster's brushes. Some of his brush packs you have to pay for, but he has tons of free ones as well. I haven't even bothered trying to make any of my own since I started using his because they just feel that good. I will point out, though, that unless you do use a current version of photoshop, these brushes will not work. Since I started using his brushes, I haven't made a single one on my own, cuz they pretty much satisfy my every itch.