I must admit that with the number of migrated faction games I play, I often can't recruit them anyway, but I've never felt the loss. Elites just seem to be a bad economy - and hardly worth it either.
You can't recruit them in many places, meaning particular settlements become the sole place you can get them (bringing all the logistics of getting them to the rest of the army). If you retrain (I try not to), you've got the reverse logistics to get them back there.
Then there's the cost; double or even triple a non-elite unit. Yet you aren't getting a lot more for your money, they may be significantly better in certain areas, but they rarely win a battle by themselves. It's still a numbers game a lot of the time past a certain minimum level of quality. Talking of numbers, they're often smaller than normal units too.
I'll illustrate the point by comparing some units who fit roughly in the same role. It's not a perfect comparison, because the elite can perform the role of "assault infantry" which few other units can.
Take the Peltastai Makedonikoi and the more regular Peltastai. The former is almost 2.5x the price of the latter, and has a smaller unit. The elite is significantly more armoured, and has 150% the overall defense, and a much higher attack stat. Better morale and discipline. However, they have half the number of javelins, and they're shorter ranged. Obviously that's because Peltastai Makedonikoi aren't skirmishers, but their loadout is the same. Lacking spears, they can't be used as anti-cavalry.
Upshot is, I'd rather have two units of Peltastai than one of Peltastai Makedonikoi. You can do a lot more with them, and that's four times as many javelins. The comparison is even worse if you take Thraikioi Peltastai; only slightly more expensive than regular Peltastai, but you can still get two for the price of one unit of PM. They're almost as heavily armoured, and as a bonus their secondary weapon is AP, making them brilliant enemy Family Member killers. Both the latter two are available as mercenaries almost everywhere, too.
With cavalry it gets even worse; most elite cavalry is ridiculously expensive, but since it's often heavy, blown after a couple of charges. Or else not a huge amount better than their non-elite version. Take Tarentine Elite and regular Hippakontistai. Once more, the elite is more than double the price of the non-elite. What you get is slightly better with their weapons, much better defense, slightly better morale. Again, unless you are stack-constrained, two of the cheaper are likely to be better. You shouldn't be using sword-armed cavalry for shock charges anyway, so the fact that the elites are more able to survive prolonged melee is kind of moot.
I can see the roleplaying reasons you might recruit elites, especially if your stack is a "royal army", or the bragging rights that you have so much money you can afford to use them, but from a functional standpoint, what's the value in elites?
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