Sure you can, as long as you meet the prestige class’s prerequisites. The Commoner class does not have any special rules about its advancement, it’s just a particularly weak base class.
It’s actually the easiest way to enter the Survivor prestige class (Savage Species), which requires that one’s highest base save bonus be lower than one’s character level. In a similar case, the Adept is the easiest way to enter the Hexer prestige class (Masters of the Wild), since it requires lightning bolt as a divine spell, and neither clerics nor druids get it, nor is it found on any Domain (amazingly).
I would comment that a common way to handle games where you start as Commoners is to have you “trade in” Commoner levels for PC-class levels, to avoid you taking pretty serious hits to your abilities relative to your nominal ECL. This is a non-issue if your DM knows how to compensate, but it might be worth mentioning as an idea to your DM.
First of all, the Prestige Class Tier List is not nearly as widely-ascribed-to as JaronK’s base class one. For one thing, it is much harder to judge a prestige class (especially ones that can vary so much depending on how you enter), and for another there are just so many more of them.
Take the Shadowsun Ninja. For a Monk, it’s a dramatic step up; for a Swordsage, it’s... a thing. There are some neat tricks possible with it (Tomb-Tainted Soul or the Undead type allow you to use the negative energy for healing while using the positive energy on your allies, so that’s indefinite healing), but ultimately it doesn’t really change much about the Swordsage’s tier.
The problem of the Master of Nine is that it requires a ton of feats. If you aren’t a Swordsage, it also requires multiclassing, but that’s not really a bad thing for initiators. In fact, judicious multiclassing helps a great deal with the feats, because one level in Cleric gets you two of the feats (Darkness or Shadow domain gets Blind-fight, Time domain gets you Improved Initiative). The unarmed Swordsage adaptation also gets you Improved Unarmed Strike, and most Swordsages want Adaptive Style anyway.
That leaves only Dodge to be picked up. Several options, including Tome of Battle’s own Desert Wind Dodge, are better than ordinary Dodge, though even the best is still weak. Still, one feat burned and the single-best-dip-in-the-game (don’t forget that Cleric 1 also gives a few spells, and Turn Undead can be used to fuel the often-excellent [Divine] and [Domain] feats) is not too high a price to pay for the excellent class features that Master of Nine offers.
The limited Dual Stance feature is not nearly as good as the Warblade’s version of the same, but it’s still awesome and you can get it way sooner than 20th level. The eight maneuvers in five levels, of course, is phenomenal, and a maneuver readied per level is insane.
If you try to get into Master of Nine as a regular, single-classed Swordsage, you’re making a huge mistake and will regret burning all of your feats that way. If you’re clever about picking up feats, though... the class can be excellent.
Side-note: you don’t lose “more” by taking another level in addition to Cleric 1 with your Swordsage levels, because other class levels count half for your initiator level. There are a lot of great options for that extra level. Fighter or Psychic Warrior could be used to get another feat, to make up for the one lost picking up (Desert Wind) Dodge. Psychic Warrior also grants you a single power – which could be expansion, for instance, a great choice. Barbarian gives a ton of stuff on level 1 as well (don’t forget to check the various alternatives for Rage for the one that best works for you).
Best Answer
Not really, until high levels. As written, it's designed to blend classes and seems to have very steep requirements such that many dips are typically necessary to enter it in any reasonable timeframe. Take a look at the shadow sun ninja, as that seems to feature in many swordsage builds.
Examining links here, here, here, and here.
The only text on master of nine seems to be:
Looking at the literature, there seem to be no builds that are strongly Swordsage and master of nine. If you're looking to be a frontline swordsage ... Here are some builds:
My suggestion, click through here and see what catches your eye.