Personally, I prefer Intercity as its ticket is valid for certain day and gives me more flexibility on the time of travel.
However, as no seat reservation is needed for Intercity, the thing I am concerned about is whether the train will be full in peak seasons (as I will travel in the summer), and I might not be able to get on the train and have to wait for the next train as a result.
Moreover, is there an alternative way to travel from Rotterdam to Amsterdam apart from taking the IC train?
The main advantage of Thalys over Intercity trains is speed: 1h10 for a Thalys vs 2h10 for an Intercity on that route. And you have a reserved seat. Regarding ticketing, the point goes to the Intercity, as you say correctly.
On the other hand, if you board the Intercity in Brussels you will be sure to have a seat. I have traveled several times on that route and never had an issue with seats. Trains can be packed in the morning rush hours (into Brussels) and in the evening rush hours (out of Brussels). Traveling in Summer (July-August) is an advantage in that respect, as there will be less traffic due to the Summer holidays.
Between Rotterdam and Amsterdam you can also opt for an Intercity Direct or a Sprinter train. The former is faster and more expensive (+ 2.30 EUR) than an IC train, whereas the latter is slower and costs the same as the IC train
