The first, and best way to begin developing a good intuitive sense of ma-ai (space, time, and distance) is to measure ma-ai at the beginning of every repetition of a partner exercise. The way that we measure ma-ai is to stand palm-to-palm with your partner, both of you standing in shizentai (natural upright posture) with unbendable arms.
Something you have to watch out for, though, is the tendancy to pay attention to uke's hand instead of his center. Remember, after you measure like this, ma-ai is the distance from uke's center to tori's center - not the distance from uke's hand to tori's center. I usually teach to measure, then have both partners drop their hands, take a breath and observe how far away your partner is, then uke attacks.
Repetition of this measuring trick will instill a fine intuitive ma-ai sense, and this ma-ai measuring exercise is applicable in aikido, judo, and karate.