Why there is a big difference in the time elapsed between the SYN and SYN-ACK and then a much lesser difference between the time elapsed from SYN-ACK and the last ACK during the TCP 3-way Handshake?
That's because you're capturing on the part of the initiator. The device that issues the first and third packets. Because of this, the time delta between the 2nd and 3rd packets should be sub-milisecond. The time between the 1st and 2nd packet will be determined by network latency.
A better thing to compare would the the 1/2 and 3/4 time deltas. They would be measuring the same thing.
There are many reasons this might be the case. How large of a difference are you measuring? What devices are you measuring to and from? One reason might be that the first packets are triggering the establishment of VPN tunnels in the network. Another reason might be that the receiving application takes longer to process the initial SYN than subsequent packets.
And while the above are reasons that things might be the case, based on the answer in your comment, @sysadmin1138's answer is correct in this case: you are capturing on the initiator, which is tilting the measurement in that direction. If you were to capture on the receiver, you'd see different results: mainly the time between the SYN-ACK and ACK would be the long one.