1) you can continue to hold your residential flats in india 

2)  Foreign nationals can invest in Indian mutual funds as Qualified Foreign Investors (QFIs)

3) you cannot  purchase any agricultural land in India  after being foreign citizen 

4) you can obtain OCI card 

5) Following benefits will be allowed to an OCI:
(i) Multiple entry, multi-purpose life long visa to visit India;
(ii) Exemption from reporting to Police authorities for any length of
stay in India; and
(iii) Parity with NRIs in financial, economic and educational fields
except in the acquisition of agricultural or plantation properties.
(iv) Registered Overseas Citizen of India shall be treated at par with NonResident-Indian in the matter of inter-country adoption of Indian children.
(v) Registered Overseas Citizens of India shall be treated at par with resident
Indian nationals in the matter of tariffs in air fares in domestic sectors in
India.
(vi) Registered Overseas Citizens of India shall be charged the same entry fee as
domestic Indian visitors to visit national parks and wildlife sanctuaries in
India
(vii) Parity with Non-Resident Indian in respect of entry fees to be charged for
visiting the national monuments, historical sites and museums in India;
Pursuing the following professions in India, in pursuance of the provisions
contained in the relevant Acts, namely:-
(a) doctors, dentists, nurses and pharmacists;
(b) advocates;
(c) architects;
(d) chartered accountants;
(viii) Parity with Non-Resident Indian to appear for the All India Pre-medical Test
or such other tests to make them eligible for admission in pursuance of the
provisions contained in the relevant Acts

NO complications except you cannot hold agriculture land, which even now you cant. 200 sq yards, dose not count as agriculture land, it`s a plot.

PIO facility has been withdrawn and merged with OCI with life long validity. NO VISA required, enjoy same facilities of resident except,1, 2, 3.

In case after retirement you want to settle in India then in that case you should not take citizenship there you should continue there on visa only when your work there is complete you can return back.

Alternatively you can take citizenship there and can apply for OCI that shall give you benifit such as multiple entery in India long stay , no reporting.

Further you can also invest in India and purchase property other then agriculture land.

For NRI's there is only restrictions for to purchase agricultural land and not Commercial Shops, Apartments Building you are free to purchase as per your capacity and now days its open 100% for FDI investments.

1. even though you are living in Japan for last 15 years, you have been filing your IT returns in India

2. that is more than sufficient. The government is only interested in its revenue and taxes from the citizen, whether he is in India or in any foreign country

3. if you want to continue to have the benefits of applying for indian jobs, vote in election and buy agricultural land [subject to FEMA regulations], you can very well apply for 'Overseas Citizen of India' or OCI

4. You obtaining a Japanese passport will not adversely affect your properties in India or the returns you get from your MF investments, so long as the applicable taxes are paid on them

5. when in future while you are still in a foreign country and you decide to sell your Indian assets, then the sale proceeds will be subjected to TDS or tax deduction at source at full rate of 20%. Ofcourse you can claim refund in case the tax deducted is in excess of your tax liability

6. the position of your agricultural land which you already bought will not change even if you acquire a Japanese passport since the land was purchased when you were holding an Indian passport 

7. you just need to continue to pay your taxes on your MF investments in respect of any dividends or capital gains on sale and also on the notional rent of the flats you have in India so long as you have not sold them and on their sale you would have to pay capital gains tax in India

8. you can mull over to open a NRO account in India for ordinary transactions in addition to your NRE account [the latter i guess enables you to remit funds to a foreign account]

Even after the considering to get the Japanese passport your properties in India will remain with you and you will have all the right to dispose the property as per your wish changing nationality does not mean that you are changing all your financial obligations in India so in case you have any liability or asset in India that will be in that and you can enjoy with facility available to Indian origin people living abroad you can dispose the property and pay the taxes accordingly as per the income tax provisions the capital gain tax entirely will be deducted by the buyer on your behalf and will be paid in income tax department accordingly.

So far as sale consideration is concerned you can repatriate all the amount as the taxes are paid on that proceeds to your Japanese bank account after converting the amount into the Japanese any other currency

Other than the things you mentioned there is nothing else. But if you will come back to india then why settle in Japan. But its ok as you can get the indian citizenship anytime.

Regards 

you need to surrender your Indian passport immediately after you acquire foreign nationality.. 

Persons with a PIO were not: eligible to vote. 

PIOs do not enjoy employment rights in Government of India services nor can they hold any constitutional office in the Government of India. 

No apart from aforesaid things no other things if affect you on the same

It will not have much effect on other factors like property and mutual funds which you have in India will not get affected by this change. 

You can also purchase residential property in India after change of citizenship.

Whether you remain as Indian citizen or want to change the citizenship to Japanese, it is purely your own decision.

Your immovable properties will remain on your name itself, you dont have to be worried about it.

You may not be able to buy agricultural landed property after you become a citizen of Japan.

 You can not take away your earnings/sale proceeds etc. from India to Japan without the  leave of the RBI.