We stayed at Embassy Suites South in February of this year. Every time I walked out the front door I had to walk through a haze of smoke. When I stood in line for the bus, inevitably some yahoo, upwind, would be busy killing himself and sharing the fumes.
If you promise a smoke free environment and a dedicated shuttle, you will get our business.
As for niche, 70 million americans suffer from allergies or asthma. I haven't found any allergy-friendly hotels in the
Disneyland area. If you provided down alternatives, no-smoking, and laminate floors (in lieu of carpet, which just can't ever really be fully cleaned between guests) you could build loyal allergy conscious following. You wouldn't need to make all the changes at once, but as you are updating and refurbishing, you could implement the change over time and as each element comes on board, you could advertise it. The no-smoking on property element would require no investment on your part, and would build a very important niche. All children, elderly persons, pregnant women, asthmatics, and individuals with suppressed immune systems should avoid cigarette smoke, so that is a nice sized group.
As to your suites, like most places, you put the kids bed behind the door that closes. I can't enjoy my vacation, with my husband, when the kids could walk in on us at any minute. Put the bunkbeds and a fold out sofa in the main room space, along with the little table and chairs. The kids can sleep in the main space and allow the grown ups a private space to do grown up things

.
With the described set up you could still sleep 6, but Mom and Dad could enjoy their vacations with activities that aren't "G" rated, and my teenagers won't be accidentally "grossed out" by the realization that they weren't immaculate conceptions.
You could become a "family friendly" hotel that also offers romance for mom and dad, and isn't that romance how they became moms and dads in the first place?
I also second the idea of having hot water pots available. I am a tea drinker, and the coffee pot just doesn't cut it. I traveled to Disney World in September, and I took my own hot pot with me to make tea. It would have been really nice to use that space in my luggage for something else.
--Eeyore's Wife