I think Thailand is way underrated and gets a bad name for nothing. I went to Thailand for my honeymoon and it was amazing. We spent 6 days in Krabi which has some of the best beaches (just type Phi Phi Islands and you'll know what I am talking about) in the world and 3 days of shopping in Bangkok and believe me, wifey loved it (especially the shopping

). You can even look at Koh Samui or Chiang Mai as good, relaxing holiday destinations. The advantage with Thailand is that you get very good value for money. The hotels we stayed in during our honeymoon were 5 star rated had all the amenities and luxuries at a fraction of the cost in India. For e.g. the resort we stayed in Krabi costed us about USD350/night but believe me a similar room in any Indian hotel or resort would not cost you less than Rs.30 - 35k. Similarly for Bangkok, we stayed at The Holiday Inn, Silom and it costed us USD75 a night. And they have some of the best hotel staff in the world, too courteous and very polite unlike their more "refined" brethren in Europe and the US. In fact I feel they easily outshine Indian hospitality in some respects. Bangkok is a very nice city to visit if people actually take time out to see it. And it has some of the best shopping in the world, a fact your wife would appreciate (trust me on this). Trouble is, most people go there with a single agenda and rarely spend time on anything else

. Also, you would not have a problem with food in Thailand as plenty of good quality decently priced Indian restaurants are available everywhere.
You have to avoid places like Phuket or Pattaya and certain places in Bangkok where the things Thailand is more famous for are right in your face. If you manage that, I feel Thailand is one of the most beautiful country in the world with amazing beaches and even amazing people and hospitality.
On the Travel agent vs self part. My suggestion is book your hotels & your flights through the travel agent but book your tours and taxis and other things once you get to the destination. You'll have a chance to shop around and get better deals due to local competition for business. And Thailand is a pretty safe country and they generally do not bother tourists so you hv no worries on that front.