How to plan a day trip to Malacca (from Kuala Lumpur)?

Try not to as it is very costly to stay at Kuala Lumpur and Malacca, a UNESCO World Heritage City has more scenic heritage areas than Kuala Lumpur. However, everyone wants to visit the iconic Petronas Twin Towers. So, let me give you all an idea how to do so.

Arrive at KLIA before 5.30am (except Mondays and major Muslim festivals)
Next, take the ERL or bus and put your luggage at any of the luggage deposit shops at KL Sentral.

Note:
You may skip this step if you choose to stay a night at Kuala Lumpur city and take the taxi or LRT directly to KLCC.

Proceed from KL Sentral by 6.30am
From KL Sentral, take the RapidKL LRT (Kelana Jaya-Gombak Line) and alight at the 5th stop - the KLCC (RapidKL LRT) station. Getting out of that station to the KLCC tower can be tricky as there are no proper signage. Try asking the persons who are working at the station kiosks for directions.

After touring the towers, have brunch at the mall within the towers which is called Suria KLCC . I would recommend the foodcourt if you can get a seat with the view overlooking the park. Otherwise, try any of the restaurants or eateries at the Concourse Level (the lowest level in the mall) which is nearest to the exit to the LRT station (see Suria KLCC's mall map). Remember to use the washrooms there as the cubicles are very clean and dry because there are no water hose attached.

Leave Suria KLCC/Petronas Twin Towers by 11.00am
From the KLCC (RapidKL LRT) station, make your way back to the KL Sentral Station and collect your luggage. From there, take the KTM train to the Bandar Tasik Selatan Bus Terminal. There are buses to Malacca (Melaka Sentral bus terminal) almost every half hour.

Arriving at Melaka Sentral by 1.30pm 
Arriving here by 1.30pm or 2.00pm will allow you to maximise your time at the Malacca as there are plenty of things to see and do during the day. From the Melaka Sentral bus terminal, take a cab to any of these hotels within the Jonker Street or Dutch Square vicinity.

Going back to KLIA or flying off from Changi Airport
If you have less than 4-5 hours prior to your departure flight or your departure flight is in the wee hours of dawn, the boutique hotels that I have listed should be able to arrange a cab to send you directly to KLIA or KLIA2. Please confirm with these hotels before making your reservations.

If you prefer to fly off from Changi Airport, there are buses during the day that travels to Singapore from Melaka Sentral bus terminal. It's usually a 4 hours journey but it will take 6 hours during major festivals. It is best that your flight from Changi Airport is late night or in the wee hours of dawn the next day. This will give you ample of time to visit the prominent places at Singapore.


Note:
To sum up this post for avid and adventurous travelers with very little time:

2D/1N (44-48 hours)
Kuala Lumpur --> Malacca (1N)--> Kuala Lumpur

2D/2N (60 or more hours)
Kuala Lumpur --> Malacca (1N) --> Singapore (1N)