Pondicherry is comparatively good. The climate; the discounted booze; the historical remains; and Beaches will give you a great experience. So, try visiting this time. Ping me for further details.
If you're a beach person then Pondicherry is the place but if you want Divinity, trekking, waterfalls then Shimoga is the best. Kunchikal falls near Shimoga is one of the the highest waterfalls in India.
Both the places have their own charm. Pondicherry is more about serene beaches and if you are an adventure junkie, loves visiting waterfalls and doing trekking, plan to Shimoga.
Both are good depending on what you are looking for. If you want to be amidst nature shimoga is the place to go. If you like beaches and walking around streets admiring the French architecture, pondicherry is the place