Based on my (admittedly limited) research, Universal hotels are only cheaper if there are four or fewer people in a room. Any more in the party and you'll need either two rooms or a suite. Compare this to WDW, which has plenty of five person moderate rooms, and they don't count an infant in a crib toward room capacity. Obviously larger families pay more for things in general, but Universal's four person room capacities versus WDW's five plus infant means that our family of six pays significantly less at WDW.
For example, we could stay at Port Orleans Riverside (pool view) for three nights in July for an undiscounted price of $261 per night ($221.85 including the Summer Room Offer, or 35% off the rack rate for military). For the same dates, only three resorts come up at Universal: Cabana Bay ($244 per night, but does not include Express Pass), Pacific Royal for $1024 per night, and Portofino Bay for $879 per night. Add in military pricing, and the PO-R room drops to approx $170 per night, and Portofino to $615.30 per night. (As a side note, we're staying in a CL PV room at the Poly for less than that Portofino room, although Portofino does look like a lovely hotel and we definitely plan to stay there sometime.)
Adding Express Pass to regular 3 day park-to-park tickets for four people in July adds $1,559.88 (+ tax) to the ticket price for a grand total after taxes of $2,811.46. We bought WDW APs (which obv include FP+, in addition to other benefits like parking and MM) for not significantly more than that.
The cost of adding Express Pass for four people to a room at Cabana Bay takes the price difference between CB and Portofino down to only a few dollars. Total cost for three nights at a Uni hotel plus EP (either paid for or included in room price) comes to approximately $2,100 once military rates are applied (park tickets not included). Compare this to $508.95 (+ tax) for three nights at PO-R on the same dates with military pricing applied (cheaper if staying at the Campsites), and obv WDW always includes FP+. (I just checked and it costs more to book two rooms at Uni than one suite on the same dates.)
Our situation is not unique. Plenty of families with 5+ members travel to Orlando. We all know that things cost more for larger families, but I think the assertion that Uni is cheaper than WDW should be qualified that it's only for families of 4 or fewer.