Firstly, I am saying absolutely nothing against either Bayethe Lodge or Table Bay Hotel (I presume you mean Table Bay not Table Top ?). If the travel agent is able to offer 3 nights free at a 5* hotel in Cape Town then,a quick check gives the cheapest rooms at £200 per night, being a cynic, I would want to know how they can do that. I presume there must be a big incentive to the Travel Agent so maybe their suggestions will be biased by this. There is an old saying that if something seems too good to be true then it then it probably is. So whilst both locations are good, I would want to know more about this deal.
Now your basic question. I have to admit I would choose a Kruger area game lodge every time. In my opinion by far the best wild-life experience in SA and most people agree this part is the highlight of their trip. Again, to be fair, Kruger is a malaria risk area, Shamwari is not.
The Garden Route is OK and we have enjoyed a few drives along it, staying between Knysna and Plettenburg at a lovely place called Lairds Lodge
(www.lairdslodge.co.za) but depends how much time you have available. I would spend a week in the Kruger area, 3/4 nights in a private game reserve and 3/4 nights outside the Park near Nelspruit or Hazyview and there would drive round the Panorama Route, beautiful scenery and also drive myself into Kruger National Park. There is nothing quite like driving along in your own car and having to stop as a herd of elephants cross the road in front of you.
I would then fly down direct from Nelspruit to Cape Town and explore the city itself, the Western Cape, and the winelands. Many many attractions and places to visit.