Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental ω-regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as reachability/safety (for disjunctive questions) and Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical ω-regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. 1 In particular improvements by polylogarithmic factors are not excluded. 2 Combinatorial here means avoiding fast matrix multiplication [33], see also the discussion in [27].2 objectives and their dual Rabin objectives [39]. A one-pair Streett objective for two sets of vertices L and U specifies that if the Büchi objective for target set L is satisfied, then also the Büchi objective for target set U has to be satisfied; in other words, a one-pair Streett objective is the disjunction of a coBüchi objective (with target set L) and a Büchi objective (with target set U ). The dual one-pair Rabin objective for two vertex sets L and U is the conjunction of a Büchi objective with target set L and a coBüchi objective with target set U . A Streett objective is the conjunction of k one-pair Streett objectives and its dual Rabin objective is the disjunction of k one-pair Rabin objectives. Algorithmic questions. The algorithmic question given a model and an objective is as follows: (a) for standard graphs, the model-checking question asks whether there is a path that satisfies the objective; and (b) for MDPs, the basic model-checking question asks whether there is a policy (or a strategy that resolves the non-deterministic choices of outgoing edges) for player...