Koopman decomposition is a non-linear generalization of eigen-decomposition, and is being increasingly utilized in the analysis of spatio-temporal dynamics. Well-known techniques such as the dynamic mode decomposition (DMD) and its linear variants provide approximations to the Koopman operator, and have been applied extensively in many fluid dynamic problems. Despite being endowed with a richer dictionary of nonlinear observables, nonlinear variants of the DMD, such as extended/kernel dynamic mode decomposition (EDMD/KDMD) are seldom applied to large-scale problems primarily due to the difficulty of discerning the Koopman invariant subspace from thousands of resulting Koopman eigenmodes. To address this issue, we propose a framework based on multi-task feature learning to extract the most informative Koopman invariant subspace by removing redundant and spurious Koopman triplets. In particular, we develop a pruning procedure that penalizes departure from linear evolution. These algorithms can be viewed as sparsity promoting extensions of EDMD/KDMD. Further, we extend KDMD to a continuous-time setting and show a relationship between the present algorithm, sparsity-promoting DMD, and an empirical criterion from the viewpoint of non-convex optimization. The effectiveness of our algorithm is demonstrated on examples ranging from simple dynamical systems to two-dimensional cylinder wake flows at different Reynolds numbers and a three-dimensional turbulent ship air-wake flow. The latter two problems are designed such that very strong nonlinear transients are present, thus requiring an accurate approximation of the Koopman operator. Underlying physical mechanisms are analyzed, with an emphasis on characterizing transient dynamics. The results are compared to existing theoretical expositions and numerical approximations.