The skitarii are a good army with lots of good options, but within those options there is a trap. Often times we are our own undoing, in that we can't help but take options when we really shouldn't and often don't need too. This will be an issue for skitarii players I suspect when it comes to the squad leaders of the skitarii infantry.
Skitarii leaders have access to quite a lot of things with special issue wargear, ranged and melee weapons, relics and squad specific stuff. This is a trap! Don't fall in to it. We have been indoctrinated by GW to see that squad leaders must have a pistol and cc weapon. No they don't! It sounds like a good idea, but really what do you gain. You get an extra cc attack at the cost of short ranged fire and less shots. This works on a decent CC character, or even on a basic space marine sgt, but skitarii are really just buffed guardsmen, or scions depending on how you look at it.
I will tell you, I wish I could just give shotguns to all my IG sgt's, it would be much more effective than an extra attack. Now IG you can make use of cc weapons in blobs, simply because there are enough bodies that all the sgts can actually hit home and do something. This really isn't the case with skitarii.
So what rule of thumb should you apply to skitarii and upgrades? Less is more. 9/10 times you don't need to give them anything, keep them stock. Really. What does a ranger squad gain by having a cc weapon and pistol, really no much and it loses on of it's long ranged attacks. While its not as bad for a vanguard squad, it still doesn't gain a whole lot in most cases. The squad will do just as well, if not better with the alpha having his carbine.
There are a few situations though where upgrades are not bad. For a dedicated anti tank vanguard squad with arc rifles, taking an arc pistol and cc weapon is not a bad choice. For cc weapon, the taser is a good choice, as its +2 S and can cause a lot of extra hits. That's the cost effective version, if you are feeling spendy the arc maul is def effective for killing vehicles, but you have to get there to use it, so keep that in mind.
For your warlord's squad, its worth giving some upgrades as well, as he will be a target simply for points. A refractor field or conversion field are both well priced and won't break the bank. A decent relic like the phosphoenix is a good plus a cheap cc weapon will give you a decent warlord with some survivability. If the price is high, go with a basic pistol and it will save you some pts here.
The other thing to consider with upgrades is what to give to the squads. When it comes to ranged weapons, always consider how they synergize with the squad. So rangers sit back and shoot at range, plasma calivers are not a good choice for them. Arc rifles are ok, and really the transuranic arquebes is the best for synergy. It does cost you though, so you may not even need it. A stock ten man squad will do their job quite well with an omnispex and thats it.
Vanguard are better for special weapons as they are going to try and get much closer to the enemy. You may be tempted to take plasma calivers, but really hold back. They are so god damn expensive. They are double the cost of plasma guns, and granted the three shots is nice, you can probably do just fine with one caliver, just one. Hold back I tell you. The arc rifle is the bang for buck special weapon, and that should be your main special weapon to go too, as it's still good against infantry and tough targets, and in mass will wreck vehicles. Again though, just because you can take three in a full squad does not mean you need too.
What I am trying to say, is that add only when it will increase effectiveness that matches the pts spent and what you lose when taking the upgrades. They are options for a reason!
GG