We are heading to Ireland the end of September and will be staying in B&B’s. We are flying in to Shannon and staying in Ennis the first night. The last night we are staying near Dublin so we can get to the airport early in the day. We have six nights to plan and it sounds from the forum that many suggest staying in a town for two to three nights. It sounds like many people like Kinsale. So we are open to suggestions for what cities to stay in and some of the best places to visit.
I assume you will have a car?
Yes we will have a car. I forgot to mention that.
In order to make the best use of your limited time I'd suggest staying close to the Connemara area. After your overnighter in Ennis you could take the scenic route via the N68/67 up along the coast towards Doolin. It's the long way around but a very pretty scenic drive with numerous possibilities for stopping for photo ops, coffee, lunch and maybe a brief stretch of the legs at the Cliff Walk at Kilkee. If the weather cooperates it's a route that's ready made for a day long meander.
We're not great fans of Galway, but basing yourselves in or near Clifden would be central for some very scenic day trips around Connemara - our favorite part of Ireland. The Sky Road scenic drive is just west of town as is the village of Cleggan from where you can take the short ferry ride over to the Island of Inishbofin ... one of Ireland's better kept secrets. There's also a loop drive that goes by Diamond Hill & Connemara National Park, Kylemore Abbey, and the beautiful village of Cong. The village is where the old John Wayne/Maureen O'hara flick "The Quiet Man" was filmed back around 1953 and it still looks like the movie set it was back in the day. Nearby is Ashford Castle which features a popular "Hawk Walk" that many here on the forum rave about. You need a reservation but you don't have to be a guest at the hotel in order to participate.
From Clifden it's about an hour's drive to the ferry landing at Rossaveal for the trip over to Inishmore ... which I highly recommend. Others here have recommended taking a flight over, but we haven't done that ourselves and so can't comment on it.
Returning to Dublin with an enroute stop at the monastic site at Clonmacnoise would give you a couple of days to explore the city before you depart.
Am afraid that any other excursions - including to Kinsale - would just have you running all over the country and you'd wind up doing drive-byes of the various sites rather than settling in at one location and enjoying the relaxed ambiance that is the essential Ireland.