OK...
Well, assuming I can't talk you into the
teensiest dip to Swordsage (free Weapon Focus with a whole load of weapons and massively improved flexibility for all sorts of reasons, not to mention the synergy with all the Tiger Claw strikes that rely on Jump checks... I had to try!) then I'll stick to the rules.
Weapon Focus: Don't do it. A +1 bonus with one weapon that doesn't scale with level? Absolutely not worth a feat, and particularly not if you're only getting it to qualify for Disemboweling Strike.
Throat Punch: Don't do it. It's too situational: great with humanoid enemy casters that can't see invisible creatures, don't have fortification, can't cast their spells silently and let you get close enough to use it... but this is a high-level game, right? Don't forget:
Ambush Feats said:
Creatures immune to extra damage from sneak attacks are also immune to the secondary effects created by ambush feats.
You're already taking a class that's subject to its main damage source being nullified by circumstances: taking a feat that's only giving you a 50% chance per round of screwing up a spellcaster in really specific circumstances is just adding to the pain.
Brachiation: Again with the really restrictive circumstances. "This ability works only in medium and dense forests". If it allowed you to ignore difficult terrain in any circumstances where you had lots of protuberances and/or dangly things, it would still be marginal... as written, it's just a waste of a feat.
Disemboweling Strike: Admittedly, pretty much anything that's vulnerable to your sudden strike is vulnerable to Con damage... but is it really worth it? You're doing 1d4 points of Con damage - once - in exchange for 4d6 points of SS damage. You're giving up an average of 14 points of damage for 1d4 points of Con... which means that on average you have to be using this on something that has 14 Hit Dice just to break even. At high levels you will be fighting things with lots of Hit Dice and I can see the appeal, but I'd probably ditch this one because you're really burning
two feats to get it. Leave the ability damage to the Clerics and Wizards, who can pull it out of thin air for no good reason a dozen times a day.
If you want something to get a bit more out of your sudden strike, consider Deadly Precision to increase the average... when you've got 10d6 per attack, it'll make a huge difference in the long run.
However, if I were playing a single-classed Ninja, I'd be looking to choose feats that gave me more flexibility and utility in and out of combat, not feats that rely entirely on my already-limited main class ability.
Max out your Wisdom and your Initiative modifier: with low hit points and medium BAB, you're going to want to be invisible as often as you can during a fight, and to capitalise on this as much as possible. Consider Spring Attack (or Shot on the Run) combined with your invisibility; unlike the spell, you don't become visible again just because you've attacked so you can move, strike and move again without provoking AoO's and keeping your enemies off-balance.
You can use poisons: do so. They fall off in utility as you increase in levels, because the DC's are flat and more creatures are either immune or likely to make the saves... but it's still worth knowing what you can do with them. Check out
Arsenic and Old Lace for an excellent primer on poisons.
If you go down the throwing-stuff route, invest in Quick Draw, a Handy Haversack and a LOT of flasks of alchemical do-baddery. Ask your DM if the extended range of alchemical substances is available so you're not limited to acid and fire. Salve of Slipperiness can give you a
grease effect, but at 1,000gp a pop it probably isn't worth it.
Give some thought to Two-Weapon Fighting as a combat technique; on those occasions you're able to do Sudden Strike damage, you want to get as much of it as possible and this is one way to do it. With thrown weapons too, why not? There are worse ideas than spamming poisoned shuriken or flasks of Alchemist's Fire. Investing in a feat chain that synergises well with your class abilities but doesn't
depend on them is good: any of the above will make you more useful in combat even when your foes are not susceptible to SS... which, depending on the campaign, could be an awful lot of the time.
Other than that, most of the recommendations I'd make would be around prestige classes to pick or base classes to dip and we've established that you're not going there
