DuplicateRepeatDistance 10000
That's should limit that POI to around 1 per map, unless you make a bigger map. You can change that if you're willing to edit the POI files.
Your next issue is they must have a place to be placed, which means you need to influence the mix of Tiles that RWG selects. If you're after skyscrapers that go into the "downtown" district, then you need more Cities. RWG offers you an option to increase the number of Cities/Towns using the UI. Also, larger maps can have more Cities/Towns. (Note that TFP's newer T5 POIs aren't targeted at the downtown. You can find them in rural and commercial districts.)
Your last option is to try to influence things via bias. Look to rwgmixer.xml:
<!-- prefab spawn weight info:
base score for a prefab is always 1,
then additions are done; score += (bias + (tier / 5)),
then score is divided by world count; score /= prefab.worldcount,
finally score is multiplied by weight and returned; return score * weight -->
<!-- weight default 1; bias default 0 -->
<prefab_spawn_adjust partial_name="lot_rural_filler" bias="5"/>
Note that the Tier figures into the formula, so higher Tier POIs already have a bias advantage over lower tier POIs. You can go nuts giving any POI with "skyscraper" in the name if you like, but remember the part about Tiles and settlements above. You need cities, then you need downtown Tiles, and then you can have places for the downtown skyscrapers to land.
It might be that you just mean "more tier 5s" instead of skyscrapers, specifically. If so, larger map and more cities is about your easy approach.